ComputeNonbondedBase2.h File Reference

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Functions
	EXCLUDED (FAST(foo bar)) EXCLUDED(MODIFIED(foo bar)) EXCLUDED(NORMAL(foo bar)) NORMAL(MODIFIED(foo bar)) ALCHPAIR(NOT_ALCHPAIR(foo bar)) ALCHPAIR(myLambda
	FEP (myLambda2=ALCH1(lambda2Up) ALCH2(lambda2Down);) myElecLambda
	FEP (myElecLambda2=ALCH1(elecLambda2Up) ALCH2(elecLambda2Down);) myVdwLambda
	FEP (myVdwLambda2=ALCH1(vdwLambda2Up) ALCH2(vdwLambda2Down);) myVdwShift
	FEP (myVdwShift2=ALCH1(vdwShift2Up) ALCH2(vdwShift2Down);)) for(k=0
	TABENERGY (register const int tabtype=lj_pars->tabletype;register int eneraddress;register BigReal r1;) Force *f_j
Variables
k< npairi;++k){TABENERGY(const int numtypes=simParams->	tableNumTypes
const float	table_spacing = simParams->tableSpacing
const int	npertype = (int) (mynearbyint(simParams->tableMaxDist / simParams->tableSpacing) + 1)
int	table_i = (r2iilist[2*k] >> 14) + r2_delta_expc
const int	j = pairlisti[k]
register const CompAtom *	p_j = p_1 + j
BigReal	diffa = r2list[k] - r2_table[table_i]
const BigReal *const	table_four_i = table_four + 16*table_i
const LJTable::TableEntry *	lj_pars
Force *	fullf_j = fullf_1 + j
BigReal	kqq = kq_i * p_j->charge
register const BigReal	p_ij_x = p_i_x - p_j->position.x
register const BigReal	p_ij_y = p_i_y - p_j->position.y
register const BigReal	p_ij_z = p_i_z - p_j->position.z

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Function Documentation

EXCLUDED (  FAST(foo bar)   )

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

FEP (  myVdwShift2  = ALCH1(vdwShift2Up) ALCH2(vdwShift2Down);  )  [pure virtual]

FEP (  myVdwLambda2  = ALCH1(vdwLambda2Up) ALCH2(vdwLambda2Down);  )

FEP (  myElecLambda2  = ALCH1(elecLambda2Up) ALCH2(elecLambda2Down);  )

FEP (  myLambda2  = ALCH1(lambda2Up) ALCH2(lambda2Down);  )

TABENERGY (  register const int  tabtype = lj_pars-, tabletype;register int eneraddress;register BigReal r1;  )

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Variable Documentation

BigReal diffa = r2list[k] - r2_table[table_i]

Definition at line 49 of file ComputeNonbondedBase2.h. Referenced by ComputeNonbondedCUDA::build_force_table(), and ExclElem::computeForce().

Force* fullf_j = fullf_1 + j

Definition at line 68 of file ComputeNonbondedBase2.h.

const int j = pairlisti[k]

Definition at line 45 of file ComputeNonbondedBase2.h. Referenced by ARestraintManager::AddForces(), GridforceGrid::allocateGridCache(), GridforceGrid::allocateGridRequestTables(), average(), OptPmeZPencil::backward_fft(), PmeZPencil::backward_fft(), Sequencer::berendsenPressure(), HomePatch::boxClosed(), build12Excls(), build13Excls(), build14Excls(), ComputeNonbondedCUDA::build_exclusions(), buildBondData(), buildExclusions(), HomePatch::buildSpanningTree(), colvar::eigenvector::calc_Jacobian_derivative(), colvar::logmsd::calc_Jacobian_derivative(), colvar::rmsd::calc_Jacobian_derivative(), cffti1(), colvar::colvar(), compute_b_spline(), PmeRealSpace::compute_forces(), OptPmeRealSpace::compute_forces(), CrosstermElem::computeForce(), ComputePme::copyPencils(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), ProxyMgr::createProxies(), Rebalancer::createSpanningTree(), crossterm_setup(), Rebalancer::decrSTLoad(), dev_nonbonded(), dev_sum_forces(), dftmod(), MigrateAtomsCombinedMsg::distribute(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), HomePatch::doPairlistCheck(), PatchMap::downstream(), PatchMap::downstream2(), ComputeNonbondedCUDA::doWork(), ComputeHomeTuples< ExclElem, Exclusion, int >::doWork(), ComputeFullDirect::doWork(), HashPool< T >::dump_tables(), dumpbench(), eigsrt(), ComputeGridForceNodeMgr::fetchGridValues(), PmeRealSpace::fill_charges(), OptPmeRealSpace::fill_charges(), WorkDistrib::fillOnePatchAtoms(), ComputeGridForce::finishForce(), ComputeNonbondedCUDA::finishWork(), flipNum(), Patch::forceBoxClosed(), forward_back_sub(), OptPmeZPencil::forward_fft(), PmeZPencil::forward_fft(), generateAtomTypeTable(), generatePmePeList(), generatePmePeList2(), getAcceptorData(), ProxyNodeAwareSpanningTreeMsg::getANewMsg(), ProxyResultVarsizeMsg::getANewMsg(), getAngleData(), getBondData(), getCrosstermData(), getDihedralData(), getDonorData(), getImproperData(), GromacsTopFile::GromacsTopFile(), AtomSigInfo::hash(), Rebalancer::incrSTLoad(), Lattice::index(), ComputePmeMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), initializePmeMap(), Matrix4::inverse(), jacobi(), Sequencer::langevinPiston(), LJTable::LJTable(), ComputeHomeTuples< ExclElem, Exclusion, int >::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(), mollify(), Matrix4::multmatrix(), Matrix4TMD::multmatrix(), NAMD_find_first_word(), RefineTorusLB::newRefine(), obj_transmult(), colvarmodule::matrix2d< colvarmodule::real, 3, 3 >::operator=(), outputCompressedFile(), outputPsfFile(), ProxyCombinedResultMsg::pack(), PatchMap::pack(), ComputeMap::pack(), PACK_MSG(), pairlist_from_pairlist(), passb(), passf(), PDB::PDB(), Patch::positionsReady(), parm::preadln(), Molecule::print_bonds(), print_Matrix4(), ComputeMap::printComputeMap(), LdbCoordinator::printLocalLdbReport(), ProxyNodeAwareSpanningTreeMsg::printOut(), PatchMap::printPatchMap(), pubdz3d(), pubz3d(), pubzd3d(), Parameters::read_energy_type_bothcubspline(), Parameters::read_energy_type_cubspline(), 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(), ComputeExtMgr::recvCoord(), ProxyMgr::recvNodeAwareSpanningTree(), ProxyMgr::recvSpanningTree(), colvarmodule::matrix2d< colvarmodule::real, 3, 3 >::reset(), PDBData::scan(), ComputeNonbondedUtil::select(), SELF(), Parameters::send_Parameters(), 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(), ComputePme::sendData(), ComputePme::sendPencils(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), sortEntries_selectionSort(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), ComputeNonbondedUtil::submitPressureProfileData(), Sequencer::submitReductions(), tcl_append_matrix(), tcl_get_matrix(), Transform::Transform(), Matrix4::transpose(), Matrix4TMD::transpose(), transpose(), ProxyCombinedResultMsg::unpack(), ProxyResultMsg::unpack(), PatchMap::unpack(), ComputeMap::unpack(), and ARestraint::UpdateCOMs().

BigReal kqq = kq_i * p_j->charge

Definition at line 115 of file ComputeNonbondedBase2.h. Referenced by ExclElem::computeForce().

const LJTable::TableEntry* lj_pars

Initial value: lj_row + 2 * p_j->vdwType MODIFIED(+ 1) Definition at line 53 of file ComputeNonbondedBase2.h. Referenced by ExclElem::computeForce().

const int npertype = (int) (mynearbyint(simParams->tableMaxDist / simParams->tableSpacing) + 1)

Definition at line 41 of file ComputeNonbondedBase2.h.

register const BigReal p_ij_x = p_i_x - p_j->position.x

Definition at line 119 of file ComputeNonbondedBase2.h.

register const BigReal p_ij_y = p_i_y - p_j->position.y

Definition at line 120 of file ComputeNonbondedBase2.h.

register const BigReal p_ij_z = p_i_z - p_j->position.z

Definition at line 121 of file ComputeNonbondedBase2.h.

register const CompAtom* p_j = p_1 + j

Definition at line 46 of file ComputeNonbondedBase2.h. Referenced by ExclElem::computeForce(), and pairlist_from_pairlist().

const BigReal* const table_four_i = table_four + 16*table_i

Definition at line 50 of file ComputeNonbondedBase2.h. Referenced by ExclElem::computeForce().

int table_i = (r2iilist[2*k] >> 14) + r2_delta_expc

Definition at line 44 of file ComputeNonbondedBase2.h. Referenced by ComputeNonbondedCUDA::build_force_table(), and ExclElem::computeForce().

const float table_spacing = simParams->tableSpacing

Definition at line 40 of file ComputeNonbondedBase2.h. Referenced by Parameters::read_ener_table(), Parameters::read_energy_type(), Parameters::read_energy_type_bothcubspline(), and Parameters::read_energy_type_cubspline().

k<npairi; ++k) { TABENERGY( const int numtypes = simParams-> tableNumTypes

Definition at line 39 of file ComputeNonbondedBase2.h.

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