ComputeNonbondedBase2.h File Reference

Go to the source code of this file.

Defines

#define p_j   (p_1+j)
#define table_four_i   (table_four + 16*table_i)
#define lj_pars   (lj_row+lj_index)
#define f_j   (f_1+j)
#define p_j   (p_1+j)
#define table_four_i   (table_four + 16*table_i)
#define lj_pars   (lj_row+lj_index)
#define f_j   (f_1+j)
#define p_j   (p_1+j)
#define table_four_i   (table_four + 16*table_i)
#define lj_pars   (lj_row+lj_index)
#define f_j   (f_1+j)

Functions

 ALCHPAIR (myLambda=ALCH1(lambdaUp) ALCH2(lambdaDown);FEP(myLambda2=ALCH1(lambda2Up) ALCH2(lambda2Down);) myElecLambda=ALCH1(elecLambdaUp) ALCH2(elecLambdaDown);FEP(myElecLambda2=ALCH1(elecLambda2Up) ALCH2(elecLambda2Down);) myVdwLambda=ALCH1(vdwLambdaUp) ALCH2(vdwLambdaDown);FEP(myVdwLambda2=ALCH1(vdwLambda2Up) ALCH2(vdwLambda2Down);) myRepLambda=ALCH1(repLambdaUp) ALCH2(repLambdaDown);FEP(myRepLambda2=ALCH1(repLambda2Up) ALCH2(repLambda2Down);) myVdwShift=ALCH1(vdwShiftUp) ALCH2(vdwShiftDown);FEP(myVdwShift2=ALCH1(vdwShift2Up) ALCH2(vdwShift2Down);)) for(k=0
 TABENERGY (register const int tabtype=-1-(lj_pars->A< 0?lj_pars->A:0);) BigReal kqq
 ALCHPAIR (const BigReal r2=r2list[k]-r2_delta;FEP(fep_vdw_forceandenergies(A, B, r2, myVdwShift, myVdwShift2, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, myVdwLambda2, alchWCAOn, myRepLambda, myRepLambda2,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_energy_2);) TI(ti_vdw_force_energy_dUdl(A, B, r2, myVdwShift, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, alchVdwShiftCoeff, alchWCAOn, myRepLambda,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_dUdl);)) ENERGY(register BigReal vdw_val
 ALCHPAIR (TI(ALCH1(vdwEnergy_ti_1) ALCH2(vdwEnergy_ti_2)+=alch_vdw_dUdl;)) INT(register BigReal vdw_dir
 NORMAL (BigReal fast_d=kqq *table_four_i[8];BigReal fast_c=kqq *table_four_i[9];BigReal fast_b=kqq *table_four_i[10];BigReal fast_a=kqq *table_four_i[11];) MODIFIED(BigReal modfckqq

Variables

k< npairi;++k){TABENERGY(const
int numtypes=simParams-> 
tableNumTypes
const float table_spacing = simParams->tableSpacing
const int npertype = (int) (namdnearbyint(simParams->tableMaxDist / simParams->tableSpacing) + 1)
int table_i = (r2iilist[2*k] >> 14) + r2_delta_expc
const int j = pairlisti[k]
BigReal diffa = r2list[k] - r2_table[table_i]
const int lj_index = 2 * p_j->vdwType MODIFIED(+ 1)
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
const BigReal A = scaling * lj_pars->A
const BigReal B = scaling * lj_pars->B
BigReal vdw_d = A * table_four_i[0] - B * table_four_i[4]
BigReal vdw_c = A * table_four_i[1] - B * table_four_i[5]
BigReal vdw_b = A * table_four_i[2] - B * table_four_i[6]
BigReal vdw_a = A * table_four_i[3] - B * table_four_i[7]
 vdwEnergy = LAM(lambda_pair *) vdw_val
 vdw_dir = ( diffa * vdw_d + vdw_c ) * diffa + vdw_b
 reduction [pairVDWForceIndex_X] = force_sign * vdw_dir * p_ij_x
BigReal fast_d = modfckqq * table_four_i[8]
BigReal fast_c = modfckqq * table_four_i[9]
BigReal fast_b = modfckqq * table_four_i[10]
BigReal fast_a = modfckqq * table_four_i[11]
register BigReal fast_dir
BigReal force_r = LAM(lambda_pair *) fast_dir

Define Documentation

#define f_j   (f_1+j)
#define f_j   (f_1+j)
#define f_j   (f_1+j)

Referenced by for().

#define lj_pars   (lj_row+lj_index)

Definition at line 107 of file ComputeNonbondedBase2.h.

#define lj_pars   (lj_row+lj_index)
#define lj_pars   (lj_row+lj_index)

Referenced by ExclElem::computeForce(), and for().

#define p_j   (p_1+j)

Definition at line 93 of file ComputeNonbondedBase2.h.

#define p_j   (p_1+j)
#define p_j   (p_1+j)

Referenced by ExclElem::computeForce(), and for().

#define table_four_i   (table_four + 16*table_i)

Definition at line 101 of file ComputeNonbondedBase2.h.

#define table_four_i   (table_four + 16*table_i)
#define table_four_i   (table_four + 16*table_i)

Referenced by ExclElem::computeForce().


Function Documentation

ALCHPAIR ( TI(ALCH1(vdwEnergy_ti_1) ALCH2(vdwEnergy_ti_2)+=alch_vdw_dUdl;)   ) 
ALCHPAIR ( const BigReal  r2 = r2list[k]-r2_delta;FEP(fep_vdw_forceandenergies(AB, r2, myVdwShift, myVdwShift2, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, myVdwLambda2, alchWCAOn, myRepLambda, myRepLambda2,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_energy_2);) TI(ti_vdw_force_energy_dUdl(AB, r2, myVdwShift, switchdist2, cutoff2, switchfactor, vdwForceSwitching, myVdwLambda, alchVdwShiftCoeff, alchWCAOn, myRepLambda,&alch_vdw_energy,&alch_vdw_force,&alch_vdw_dUdl);)  ) 
ALCHPAIR ( myLambda  = ALCH1(lambdaUp) ALCH2(lambdaDown);FEP(myLambda2=ALCH1(lambda2Up) ALCH2(lambda2Down);) myElecLambda=ALCH1(elecLambdaUp) ALCH2(elecLambdaDown);FEP(myElecLambda2=ALCH1(elecLambda2Up) ALCH2(elecLambda2Down);) myVdwLambda=ALCH1(vdwLambdaUp) ALCH2(vdwLambdaDown);FEP(myVdwLambda2=ALCH1(vdwLambda2Up) ALCH2(vdwLambda2Down);) myRepLambda=ALCH1(repLambdaUp) ALCH2(repLambdaDown);FEP(myRepLambda2=ALCH1(repLambda2Up) ALCH2(repLambda2Down);) myVdwShift=ALCH1(vdwShiftUp) ALCH2(vdwShiftDown);FEP(myVdwShift2=ALCH1(vdwShift2Up) ALCH2(vdwShift2Down);)  )  [pure virtual]

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

NORMAL ( BigReal  fast_d = kqq *table_four_i[8];BigReal fast_c=kqq *table_four_i[9];BigReal fast_b=kqq *table_four_i[10];BigReal fast_a=kqq *table_four_i[11];  ) 
TABENERGY ( register const int  tabtype = -1-(lj_pars->A< 0?lj_pars->A:0);  ) 

Variable Documentation

const BigReal A = scaling * lj_pars->A
const BigReal B = scaling * lj_pars->B
BigReal diffa = r2list[k] - r2_table[table_i]
fast_a = modfckqq * table_four_i[11]

Definition at line 330 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

fast_b = modfckqq * table_four_i[10]

Definition at line 329 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce(), and for().

fast_c = modfckqq * table_four_i[9]

Definition at line 328 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

BigReal fast_d = modfckqq * table_four_i[8]

Definition at line 327 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

register BigReal fast_dir
Initial value:

Definition at line 471 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce(), and for().

BigReal force_r = LAM(lambda_pair *) fast_dir

Definition at line 474 of file ComputeNonbondedBase2.h.

Referenced by for().

const int j = pairlisti[k]

Definition at line 91 of file ComputeNonbondedBase2.h.

Referenced by ComputePmeCUDAMgr::activate_pencils(), Controller::adaptTempInit(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), ARestraintManager::AddForces(), after_backend_init(), anterpolation(), CudaComputeNonbonded::assignPatches(), ComputeNonbondedCUDA::assignPatches(), CudaComputeNonbonded::assignPatchesOnPe(), PmeZPencil::backward_fft(), Sequencer::berendsenPressure(), bin_evaluation_1away(), bin_evaluation_k_away(), bitshiftTileListDepth(), HomePatch::boxClosed(), build12Excls(), build13Excls(), build14Excls(), ComputeNonbondedCUDA::build_exclusions(), Molecule::build_go_arrays(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), ComputeNonbondedCUDA::build_lj_table(), buildBondData(), buildExclusions(), CollectProxyVectorInstance::buildMsg(), WorkDistrib::buildNodeAwarePeOrdering(), buildSortKeys(), HomePatch::buildSpanningTree(), buildTileListsBBKernel(), ExclusionSignature::buildTuples(), calc_one_theta(), calc_theta_dtheta(), ParallelIOMgr::calcAtomsInEachPatch(), Sequencer::calcFixVirial(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), cffti1(), ComputePmeMgr::chargeGridReady(), MsmGridCutoffKernel< Float, Float >::compute(), GridforceFullSubGrid::compute_b(), compute_b_spline(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_d3V(), GridforceFullBaseGrid::compute_dV(), MsmC1HermiteGridCutoff::compute_specialized(), GridforceFullBaseGrid::compute_V(), GridforceLiteGrid::compute_VdV(), GridforceFullBaseGrid::compute_VdV(), CrosstermElem::computeForce(), ComputePmeMgr::copyPencils(), ComputeMgr::createComputes(), Rebalancer::createSpanningTree(), crossterm_setup(), cuda_init_bspline_coeffs(), Rebalancer::decrSTLoad(), dftmod(), MigrateAtomsCombinedMsg::distribute(), ComputeSphericalBC::doForce(), ComputeLCPO::doForce(), ComputeCylindricalBC::doForce(), ComputeMsmMgr::doneVirialContrib(), PatchMap::downstream(), ComputeNonbondedCUDA::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), ComputeFullDirect::doWork(), HashPool< T >::dump_tables(), dumpbench(), msm::Grid< BlockDiagram >::extract(), msm::GridFixed< T, N >::extract(), PmeAtomFiler::fileAtoms(), fillSortKeys(), ComputeNonbondedCUDA::finishWork(), flipNum(), for(), Patch::forceBoxClosed(), forward_back_sub(), PmeZPencil::forward_fft(), GBIS_P1_Kernel(), GBIS_P2_Kernel(), GBIS_P3_Kernel(), generateAtomTypeTable(), GridforceFullMainGrid::get_all_gridvals(), DihedralTable::getIndex(), DihedralTable::getParams(), gridcutoff(), GromacsTopFile::GromacsTopFile(), AtomSigInfo::hash(), if(), Rebalancer::incrSTLoad(), Lattice::index(), DeviceCUDA::initialize(), ComputePmeCUDADevice::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeCUDAMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), ComputePmeCUDADevice::initializePatches(), ParallelIOMgr::integrateMigratedAtoms(), interpolation(), Matrix4::inverse(), Sequencer::langevinPiston(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), lu_decomp_nopivot(), main(), Rebalancer::makeHeaps(), PatchMap::makePatches(), Rebalancer::makeTwoHeaps(), ComputePmeCUDADevice::mergeForcesOnPatch(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Matrix4Symmetry::multmatrix(), Matrix4::multmatrix(), Matrix4TMD::multmatrix(), NAMD_find_first_word(), Sequencer::newMinimizeDirection(), RefineTorusLB::newRefine(), obj_transmult(), msm::Grid< BlockDiagram >::operator+=(), msm::GridFixed< T, N >::operator+=(), outputCompressedFile(), PatchMap::pack(), 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(), 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ComputeNonbondedUtil::select(), Molecule::send_GoMolecule(), PmeYPencil::send_subset_trans(), PmeZPencil::send_subset_trans(), PmeYPencil::send_subset_untrans(), PmeXPencil::send_subset_untrans(), PmeYPencil::send_trans(), PmeZPencil::send_trans(), PmeZPencil::send_ungrid(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ParallelIOMgr::sendAtomsToHomePatchProcs(), ComputePmeMgr::sendDataPart(), ComputePmeMgr::sendPencils(), ComputePmeMgr::sendPencilsPart(), ComputePmeMgr::sendTransSubset(), ComputePmeMgr::sendUngridSubset(), ComputePmeMgr::sendUntransSubset(), msm::FoldFactor::set(), GridforceFullMainGrid::set_all_gridvals(), MsmC1HermiteGridCutoff::setup(), MsmGridCutoff::setup(), setup_bins_k_away(), setup_grids(), sortEntries_selectionSort(), WorkDistrib::sortPmePes(), NamdHybridLB::splitComputes(), ComputeMgr::splitComputes(), storeInReverse(), CollectionMgr::submitForces(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), 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const int lj_index = 2 * p_j->vdwType MODIFIED(+ 1)

Definition at line 106 of file ComputeNonbondedBase2.h.

Referenced by for().

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

Definition at line 87 of file ComputeNonbondedBase2.h.

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

Definition at line 196 of file ComputeNonbondedBase2.h.

Referenced by for().

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

Definition at line 197 of file ComputeNonbondedBase2.h.

Referenced by for().

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

Definition at line 198 of file ComputeNonbondedBase2.h.

Referenced by for().

reduction[pairVDWForceIndex_Z] = force_sign * vdw_dir * p_ij_x

Definition at line 311 of file ComputeNonbondedBase2.h.

int table_i = (r2iilist[2*k] >> 14) + r2_delta_expc
const float table_spacing = simParams->tableSpacing

Definition at line 86 of file ComputeNonbondedBase2.h.

Referenced by Parameters::read_ener_table().

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

Definition at line 85 of file ComputeNonbondedBase2.h.

BigReal vdw_a = A * table_four_i[3] - B * table_four_i[7]

Definition at line 215 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

BigReal vdw_b = A * table_four_i[2] - B * table_four_i[6]

Definition at line 214 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce(), and for().

BigReal vdw_c = A * table_four_i[1] - B * table_four_i[5]

Definition at line 213 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

BigReal vdw_d = A * table_four_i[0] - B * table_four_i[4]

Definition at line 212 of file ComputeNonbondedBase2.h.

Referenced by ExclElem::computeForce().

Definition at line 309 of file ComputeNonbondedBase2.h.

vdwEnergy = LAM(lambda_pair *) vdw_val

Definition at line 287 of file ComputeNonbondedBase2.h.

Referenced by for().


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