NAMD
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#include <Vector.h>
Public Member Functions | |
Vector (void) | |
Vector (BigReal newx, BigReal newy, BigReal newz) | |
Vector (BigReal newv) | |
Vector (const FloatVector &v) | |
BigReal & | operator[] (int i) |
Vector & | operator= (const BigReal &v2) |
void | operator+= (const Vector &v2) |
void | operator-= (const Vector &v2) |
void | operator*= (const BigReal &v2) |
void | operator/= (const BigReal &v2) |
BigReal | length (void) const |
BigReal | length2 (void) const |
BigReal | rlength (void) |
Vector | unit (void) const |
void | cross (const Vector &v2) |
BigReal | dot (const Vector &v2) |
Bool | set (const char *s) |
Public Attributes | |
BigReal | x |
BigReal | y |
BigReal | z |
Friends | |
int | operator== (const Vector &v1, const Vector &v2) |
int | operator!= (const Vector &v1, const Vector &v2) |
Vector | operator+ (const Vector &v1, const Vector &v2) |
Vector | operator- (const Vector &v1) |
Vector | operator- (const Vector &v1, const Vector &v2) |
BigReal | operator* (const Vector &v1, const Vector &v2) |
Vector | operator* (const BigReal &f, const Vector &v1) |
Vector | operator* (const Vector &v1, const BigReal &f) |
Vector | operator/ (const Vector &v1, const BigReal &f) |
Vector | cross (const Vector &v1, const Vector &v2) |
Vector | cross (const Real &k, const Vector &v1, const Vector &v2) |
Vector | cross (const BigReal &k, const Vector &v1, const Vector &v2) |
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inline |
Definition at line 169 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(), proc_anglegrad(), proc_dihedralgrad(), proc_getangle(), proc_getdihedral(), ComputeQM::processFullQM(), Lattice::set(), unit(), and vec_rotation_matrix().
Definition at line 173 of file Vector.h.
Referenced by Sequencer::calcKineticEnergy(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcUSR(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), 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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inline |
Definition at line 177 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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inline |
Definition at line 228 of file Vector.h.
References FALSE, TRUE, x, y, and z.
Referenced by colvarproxy_namd::calculate(), and ParseOptions::get().
Definition at line 182 of file Vector.h.
References length(), Vector(), x, y, and z.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcUSR(), PmeKSpace::compute_energy(), ComputeStir::ComputeStir(), HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), Sequencer::minimizeMoveDownhill(), ComputeQMMgr::recvPntChrg(), settle1(), settlev(), PatchMap::sizeGrid(), and Sequencer::submitMinimizeReductions().
BigReal Vector::x |
Definition at line 66 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeRestraints::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), 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(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_x::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeFmmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().
BigReal Vector::y |
Definition at line 66 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), 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(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_y::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().
BigReal Vector::z |
Definition at line 66 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeNonbondedPair::doForce(), ComputeSphericalBC::doForce(), ComputeNonbondedSelf::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), 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(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_z::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().