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Definition at line 45 of file ComputeNonbondedBase2.h.
Referenced by Controller::adaptTempInit(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), ARestraintManager::AddForces(), anterpolation(), ComputeNonbondedCUDA::assignPatches(), average(), OptPmeZPencil::backward_fft(), PmeZPencil::backward_fft(), Sequencer::berendsenPressure(), bin_evaluation_1away(), bin_evaluation_k_away(), HomePatch::boxClosed(), build12Excls(), build13Excls(), build14Excls(), colvar::build_atom_list(), ComputeNonbondedCUDA::build_exclusions(), Molecule::build_go_arrays(), Molecule::build_go_sigmas(), ComputeNonbondedCUDA::build_lj_table(), buildBondData(), buildExclusions(), HomePatch::buildSpanningTree(), ExclusionSignature::buildTuples(), colvar::calc(), colvar::selfcoordnum::calc_gradients(), colvar::eigenvector::calc_Jacobian_derivative(), colvar::logmsd::calc_Jacobian_derivative(), colvar::rmsd::calc_Jacobian_derivative(), colvar::selfcoordnum::calc_value(), ParallelIOMgr::calcAtomsInEachPatch(), ComputeNonbondedUtil::calcGBIS(), cffti1(), colvar::colvar(), GridforceFullSubGrid::compute_b(), compute_b_spline(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_d3V(), GridforceFullBaseGrid::compute_dV(), PmeRealSpace::compute_forces(), OptPmeRealSpace::compute_forces(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_V(), GridforceFullBaseGrid::compute_VdV(), CrosstermElem::computeForce(), ComputePme::ComputePme(), ComputePme::copyPencils(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), PatchProxyListMsg::createPatchProxyListMsg(), ProxyMgr::createProxies(), Rebalancer::createSpanningTree(), crossterm_setup(), cuda_initialize(), Rebalancer::decrSTLoad(), HomePatch::depositMigration(), dev_sum_forces(), dftmod(), MigrateAtomsCombinedMsg::distribute(), HomePatch::doAtomMigration(), ComputeSphericalBC::doForce(), ComputeLCPO::doForce(), ComputeCylindricalBC::doForce(), HomePatch::doPairlistCheck(), PatchMap::downstream(), ComputeNonbondedCUDA::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), ComputeFullDirect::doWork(), HashPool< T >::dump_tables(), dumpbench(), eigsrt(), PmeRealSpace::fill_charges(), OptPmeRealSpace::fill_charges(), ComputeNonbondedCUDA::finishWork(), flipNum(), Patch::forceBoxClosed(), forward_back_sub(), OptPmeZPencil::forward_fft(), PmeZPencil::forward_fft(), ProxyCombinedResultMsg::fromRaw(), GBIS_Atom_Reduction_Kernel(), GBIS_Force_Reduction_Kernel(), GBIS_P1_Kernel(), GBIS_P2_Kernel(), GBIS_P3_Kernel(), generateAtomTypeTable(), generatePmePeList(), generatePmePeList2(), GridforceFullMainGrid::get_all_gridvals(), ProxyNodeAwareSpanningTreeMsg::getANewMsg(), ProxyResultVarsizeMsg::getANewMsg(), gridcutoff(), GromacsTopFile::GromacsTopFile(), AtomSigInfo::hash(), ijpair::ijpair(), Rebalancer::incrSTLoad(), Lattice::index(), ComputePmeMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), initializePmeMap(), ParallelIOMgr::integrateMigratedAtoms(), interpolation(), Matrix4::inverse(), jacobi(), Sequencer::langevinPiston(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), lu_decomp_nopivot(), lubksb(), ludcmp(), main(), PatchMap::makePatches(), OptPmeZPencil::many_to_many_recv_grid(), OptPmeXPencil::many_to_many_recv_trans(), OptPmeYPencil::many_to_many_recv_trans(), OptPmeZPencil::many_to_many_recv_untrans(), OptPmeYPencil::many_to_many_recv_untrans(), OptPmeYPencil::many_to_many_send(), OptPmeZPencil::many_to_many_send_trans(), OptPmeZPencil::many_to_many_send_ungrid(), OptPmeXPencil::many_to_many_send_untrans(), colvarmodule::matrix2d< colvarmodule::real, 3, 3 >::matrix2d(), Sequencer::minimizeMoveDownhill(), mollify(), Matrix4Symmetry::multmatrix(), Matrix4::multmatrix(), Matrix4TMD::multmatrix(), NAMD_find_first_word(), Sequencer::newMinimizeDirection(), RefineTorusLB::newRefine(), obj_transmult(), cr_sortop::operator()(), colvarmodule::matrix2d< colvarmodule::real, 3, 3 >::operator=(), outputCompressedFile(), outputProxyTree(), PACK_MSG(), pairlist_from_pairlist(), pairlistFromAll(), passb(), passf(), PDB::PDB(), Patch::positionsReady(), HomePatch::positionsReady(), parm::preadln(), Molecule::print_go_params(), Molecule::print_go_sigmas(), print_Matrix4(), ComputeMap::printComputeMap(), LdbCoordinator::printLocalLdbReport(), ProxyNodeAwareSpanningTreeMsg::printOut(), PatchMap::printPatchMap(), prolongation(), prolongation_factored(), pubdz3d(), pubz3d(), pubzd3d(), Parameters::read_energy_type_bothcubspline(), Parameters::read_energy_type_cubspline(), Molecule::read_go_file(), ParallelIOMgr::readPerAtomInfo(), Molecule::receive_GoMolecule(), Parameters::receive_Parameters(), OptPmeZPencil::recv_grid(), PmeZPencil::recv_grid(), OptPmeXPencil::recv_trans(), OptPmeYPencil::recv_trans(), PmeXPencil::recv_trans(), PmeYPencil::recv_trans(), OptPmeZPencil::recv_untrans(), OptPmeYPencil::recv_untrans(), PmeZPencil::recv_untrans(), PmeYPencil::recv_untrans(), ParallelIOMgr::recvAtomsToHomePatchProcs(), ComputeMsmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ComputeExtMgr::recvCoord(), ProxyMgr::recvNodeAwareSpanningTree(), ProxyMgr::recvPatchProxyInfo(), ProxyMgr::recvSpanningTree(), LdbCoordinator::requiredProxies(), colvarmodule::matrix2d< colvarmodule::real, 3, 3 >::reset(), restriction(), restriction_factored(), PDBData::scan(), ComputeNonbondedUtil::select(), SELF(), Molecule::send_GoMolecule(), Parameters::send_Parameters(), PmeYPencil::send_subset_trans(), PmeZPencil::send_subset_trans(), PmeYPencil::send_subset_untrans(), PmeXPencil::send_subset_untrans(), OptPmeYPencil::send_trans(), OptPmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeZPencil::send_trans(), OptPmeZPencil::send_ungrid(), PmeZPencil::send_ungrid(), OptPmeYPencil::send_untrans(), OptPmeXPencil::send_untrans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ParallelIOMgr::sendAtomsToHomePatchProcs(), ComputePme::sendData(), ComputePme::sendPencils(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), GridforceFullMainGrid::set_all_gridvals(), setup_bins_k_away(), setup_grids(), sortEntries_selectionSort(), ComputeMgr::splitComputes(), CollectionMgr::submitForces(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), ComputeNonbondedUtil::submitPressureProfileData(), Sequencer::submitReductions(), tcl_append_matrix(), tcl_get_matrix(), ProxyCombinedResultMsg::toRaw(), Transform::Transform(), Matrix4Symmetry::transpose(), Matrix4::transpose(), Matrix4TMD::transpose(), transpose(), ProxyResultMsg::unpack(), ARestraint::UpdateCOMs(), and ParallelIOMgr::updateMolInfo(). |
