NAMD
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#include <ComputeNonbondedUtil.h>
Public Types | |
enum | { exclChecksumIndex, pairlistWarningIndex, electEnergyIndex, fullElectEnergyIndex, vdwEnergyIndex, goNativeEnergyIndex, goNonnativeEnergyIndex, groLJEnergyIndex, groGaussEnergyIndex, electEnergyIndex_s, fullElectEnergyIndex_s, vdwEnergyIndex_s, electEnergyIndex_ti_1, fullElectEnergyIndex_ti_1, vdwEnergyIndex_ti_1, electEnergyIndex_ti_2, fullElectEnergyIndex_ti_2, vdwEnergyIndex_ti_2, TENSOR =(virialIndex), TENSOR =(virialIndex), VECTOR =(pairVDWForceIndex), VECTOR =(pairVDWForceIndex), reductionDataSize } |
Public Member Functions | |
ComputeNonbondedUtil () | |
~ComputeNonbondedUtil () | |
void | calcGBIS (nonbonded *params, GBISParamStruct *gbisParams) |
Definition at line 243 of file ComputeNonbondedUtil.h.
anonymous enum |
Definition at line 272 of file ComputeNonbondedUtil.h.
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Definition at line 247 of file ComputeNonbondedUtil.h.
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Definition at line 248 of file ComputeNonbondedUtil.h.
Definition at line 249 of file ComputeNonbondedUtil.C.
References NAMD_bug().
Referenced by select().
Referenced by select().
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Referenced by select().
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void ComputeNonbondedUtil::calcGBIS | ( | nonbonded * | params, |
GBISParamStruct * | gbisParams | ||
) |
Definition at line 261 of file ComputeGBIS.C.
References GBISParamStruct::a_cut, GBISParamStruct::bornRad, CalcDHPair(), CalcHPair(), CompAtom::charge, COULOMB, GBISParamStruct::cutoff, DA, DB, DC, DD, DE, GBISParamStruct::dEdaSum, GBISParamStruct::dHdrPrefix, GBISParamStruct::doEnergy, GBISParamStruct::doFullElectrostatics, GBISParamStruct::doSmoothing, GBISParamStruct::epsilon_p, GBISParamStruct::epsilon_s, nonbonded::ff, FS_MAX, nonbonded::fullf, GBISParamStruct::gbInterEnergy, GBISParamStruct::gbisPhase, GBISParamStruct::gbisStepPairlists, GBISParamStruct::gbSelfEnergy, h1(), h2(), CompAtomExt::id, GBISParamStruct::intRad, GBISParamStruct::kappa, nonbonded::minPart, Pairlists::nextlist(), CompAtom::nonbondedGroupSize, nonbonded::numAtoms, nonbonded::numParts, GBISParamStruct::numPatches, nonbonded::offset, nonbonded::p, pairlistFromAll(), nonbonded::pExt, CompAtom::position, GBISParamStruct::psiSum, Pairlists::reset(), scaling, GBISParamStruct::sequence, TA, TB, TC, TD, TE, Vector::x, Vector::y, Vector::z, and ZERO.
Referenced by ComputeNonbondedPair::doForce(), and ComputeNonbondedSelf::doForce().
Definition at line 253 of file ComputeNonbondedUtil.C.
References A, A12_f, A6_f, accelMDOn, SimParameters::accelMDOn, alchDecouple, SimParameters::alchDecouple, alchFepOn, SimParameters::alchFepOn, alchThermIntOn, SimParameters::alchThermIntOn, alchVdwShiftCoeff, SimParameters::alchVdwShiftCoeff, alchWCAOn, SimParameters::alchWCAOn, B, B12_f, B6_f, c0, C1, c1, C12_f, C2, c3, c5, c6, C6_f, c7, c8, calc_error(), calc_pair(), calc_pair_energy(), calc_pair_energy_fep(), calc_pair_energy_fullelect(), calc_pair_energy_fullelect_fep(), calc_pair_energy_fullelect_go(), calc_pair_energy_fullelect_int(), calc_pair_energy_fullelect_les(), calc_pair_energy_fullelect_pprof(), calc_pair_energy_fullelect_tabener(), calc_pair_energy_fullelect_ti(), calc_pair_energy_go(), calc_pair_energy_int(), calc_pair_energy_les(), calc_pair_energy_merge_fullelect(), calc_pair_energy_merge_fullelect_fep(), calc_pair_energy_merge_fullelect_go(), calc_pair_energy_merge_fullelect_int(), calc_pair_energy_merge_fullelect_les(), calc_pair_energy_merge_fullelect_pprof(), calc_pair_energy_merge_fullelect_tabener(), calc_pair_energy_merge_fullelect_ti(), calc_pair_energy_pprof(), calc_pair_energy_slow_fullelect(), calc_pair_energy_slow_fullelect_fep(), calc_pair_energy_slow_fullelect_go(), calc_pair_energy_slow_fullelect_les(), calc_pair_energy_slow_fullelect_pprof(), calc_pair_energy_slow_fullelect_tabener(), calc_pair_energy_slow_fullelect_ti(), calc_pair_energy_tabener(), calc_pair_energy_ti(), calc_pair_fullelect(), calc_pair_fullelect_go(), calc_pair_fullelect_les(), calc_pair_fullelect_pprof(), calc_pair_fullelect_tabener(), calc_pair_fullelect_ti(), calc_pair_go(), calc_pair_les(), calc_pair_merge_fullelect(), calc_pair_merge_fullelect_go(), calc_pair_merge_fullelect_les(), calc_pair_merge_fullelect_pprof(), calc_pair_merge_fullelect_tabener(), calc_pair_merge_fullelect_ti(), calc_pair_pprof(), calc_pair_slow_fullelect(), calc_pair_slow_fullelect_go(), calc_pair_slow_fullelect_les(), calc_pair_slow_fullelect_pprof(), calc_pair_slow_fullelect_tabener(), calc_pair_slow_fullelect_ti(), calc_pair_tabener(), calc_pair_ti(), calc_self(), calc_self_energy(), calc_self_energy_fep(), calc_self_energy_fullelect(), calc_self_energy_fullelect_fep(), calc_self_energy_fullelect_go(), calc_self_energy_fullelect_int(), calc_self_energy_fullelect_les(), calc_self_energy_fullelect_pprof(), calc_self_energy_fullelect_tabener(), calc_self_energy_fullelect_ti(), calc_self_energy_go(), calc_self_energy_int(), calc_self_energy_les(), calc_self_energy_merge_fullelect(), calc_self_energy_merge_fullelect_fep(), calc_self_energy_merge_fullelect_go(), calc_self_energy_merge_fullelect_int(), calc_self_energy_merge_fullelect_les(), calc_self_energy_merge_fullelect_pprof(), calc_self_energy_merge_fullelect_tabener(), calc_self_energy_merge_fullelect_ti(), calc_self_energy_pprof(), calc_self_energy_slow_fullelect(), calc_self_energy_slow_fullelect_fep(), calc_self_energy_slow_fullelect_go(), calc_self_energy_slow_fullelect_les(), calc_self_energy_slow_fullelect_pprof(), calc_self_energy_slow_fullelect_tabener(), calc_self_energy_slow_fullelect_ti(), calc_self_energy_tabener(), calc_self_energy_ti(), calc_self_fullelect(), calc_self_fullelect_go(), calc_self_fullelect_les(), calc_self_fullelect_pprof(), calc_self_fullelect_tabener(), calc_self_fullelect_ti(), calc_self_go(), calc_self_les(), calc_self_merge_fullelect(), calc_self_merge_fullelect_go(), calc_self_merge_fullelect_les(), calc_self_merge_fullelect_pprof(), calc_self_merge_fullelect_tabener(), calc_self_merge_fullelect_ti(), calc_self_pprof(), calc_self_slow_fullelect(), calc_self_slow_fullelect_go(), calc_self_slow_fullelect_les(), calc_self_slow_fullelect_pprof(), calc_self_slow_fullelect_tabener(), calc_self_slow_fullelect_ti(), calc_self_tabener(), calc_self_ti(), calcFullPair, calcFullPairEnergy, calcFullSelf, calcFullSelfEnergy, calcMergePair, calcMergePairEnergy, calcMergeSelf, calcMergeSelfEnergy, calcPair, calcPairEnergy, calcSelf, calcSelfEnergy, calcSlowPair, calcSlowPairEnergy, calcSlowSelf, calcSlowSelfEnergy, Parameters::columnsize, columnsize, commOnly, SimParameters::commOnly, corr_table, SimParameters::cutoff, cutoff, cutoff2, cutoff2_f, cutoff_3, cutoff_3_f, cutoff_6, cutoff_6_f, SimParameters::dielectric, dielectric_1, drudeNbthole, SimParameters::drudeNbtholeCut, SimParameters::drudeOn, endi(), ewaldcof, SimParameters::exclude, fast_table, SimParameters::fixedAtomsForces, fixedAtomsOn, SimParameters::fixedAtomsOn, SimParameters::FMAOn, SimParameters::FMMOn, full_table, SimParameters::fullDirectOn, Parameters::get_num_vdw_params(), LJTable::get_table_dim(), Parameters::get_vdw_pair_params(), Parameters::get_vdw_params(), SimParameters::goForcesOn, goForcesOn, SimParameters::goGroPair, goGroPair, SimParameters::goMethod, goMethod, iERROR(), iINFO(), iout, k_vdwa, k_vdwa_f, k_vdwb, k_vdwb_f, lambda_table, lesFactor, SimParameters::lesFactor, lesOn, SimParameters::lesOn, lesScaling, SimParameters::limitDist, ljTable, SimParameters::longSplitting, SimParameters::martiniSwitching, mol, Node::molecule, SimParameters::MSMOn, SimParameters::MSMSplit, NAMD_bug(), NAMD_die(), SimParameters::nonbondedScaling, Node::Object(), pairInteractionOn, SimParameters::pairInteractionOn, pairInteractionSelf, SimParameters::pairInteractionSelf, Node::parameters, pi_ewaldcof, SimParameters::PMEEwaldCoefficient, SimParameters::PMEOn, pressureProfileAtomTypes, SimParameters::pressureProfileAtomTypes, pressureProfileOn, SimParameters::pressureProfileOn, pressureProfileSlabs, SimParameters::pressureProfileSlabs, qmForcesOn, SimParameters::qmForcesOn, r2_delta, r2_delta_1, r2_delta_exp, r2_table, Parameters::rowsize, rowsize, SimParameters::scale14, scale14, SCALED14, scaling, scor_table, send_build_cuda_force_table(), SHARP, Node::simParameters, simParams, slow_table, SimParameters::soluteScalingOn, SPLIT_C1, SPLIT_C2, SPLIT_MARTINI, SPLIT_NONE, SPLIT_SHIFT, SPOLY, SimParameters::switchingActive, SimParameters::switchingDist, switchOn, switchOn2, switchOn_1, switchOn_f, table_alloc, Parameters::table_ener, table_ener, table_length, table_noshort, table_short, SimParameters::tabulatedEnergies, SimParameters::useAVXTiles, SimParameters::useCUDA2, v_vdwa, v_vdwa_f, v_vdwb, v_vdwb_f, vdw_switch_mode, VDW_SWITCH_MODE_ENERGY, VDW_SWITCH_MODE_FORCE, VDW_SWITCH_MODE_MARTINI, vdwa_table, vdwb_table, SimParameters::vdwForceSwitching, vdwForceSwitching, SimParameters::vdwGeometricSigma, x, and XPLOR.
Referenced by SimParameters::nonbonded_select(), and SimParameters::scriptSet().
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Definition at line 428 of file ComputeNonbondedUtil.h.
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Definition at line 218 of file ComputeNonbondedUtil.C.
References SubmitReduction::add(), pressureProfileAtomTypes, and pressureProfileSlabs.
Referenced by ComputeNonbondedPair::doForce(), and ComputeNonbondedSelf::doForce().
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Definition at line 186 of file ComputeNonbondedUtil.C.
References ADD_TENSOR, ADD_VECTOR, electEnergyIndex, electEnergyIndex_s, electEnergyIndex_ti_1, electEnergyIndex_ti_2, exclChecksumIndex, fullElectEnergyIndex, fullElectEnergyIndex_s, fullElectEnergyIndex_ti_1, fullElectEnergyIndex_ti_2, goNativeEnergyIndex, goNonnativeEnergyIndex, groGaussEnergyIndex, groLJEnergyIndex, SubmitReduction::item(), pairlistWarningIndex, REDUCTION_COMPUTE_CHECKSUM, REDUCTION_ELECT_ENERGY, REDUCTION_ELECT_ENERGY_F, REDUCTION_ELECT_ENERGY_SLOW, REDUCTION_ELECT_ENERGY_SLOW_F, REDUCTION_ELECT_ENERGY_SLOW_TI_1, REDUCTION_ELECT_ENERGY_SLOW_TI_2, REDUCTION_ELECT_ENERGY_TI_1, REDUCTION_ELECT_ENERGY_TI_2, REDUCTION_EXCLUSION_CHECKSUM, REDUCTION_GO_NATIVE_ENERGY, REDUCTION_GO_NONNATIVE_ENERGY, REDUCTION_GRO_GAUSS_ENERGY, REDUCTION_GRO_LJ_ENERGY, REDUCTION_LJ_ENERGY, REDUCTION_LJ_ENERGY_F, REDUCTION_LJ_ENERGY_TI_1, REDUCTION_LJ_ENERGY_TI_2, REDUCTION_PAIRLIST_WARNINGS, vdwEnergyIndex, vdwEnergyIndex_s, vdwEnergyIndex_ti_1, and vdwEnergyIndex_ti_2.
Referenced by ComputeNonbondedPair::doForce(), and ComputeNonbondedSelf::doForce().
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Definition at line 373 of file ComputeNonbondedUtil.h.
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Definition at line 370 of file ComputeNonbondedUtil.h.
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Definition at line 382 of file ComputeNonbondedUtil.h.
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Definition at line 256 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 257 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 258 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 259 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 261 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 262 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 263 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 264 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 251 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 252 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 253 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 254 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 266 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 267 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and select().
Definition at line 268 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
Definition at line 269 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedSelf::doForce(), and select().
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Definition at line 297 of file ComputeNonbondedUtil.h.
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Definition at line 286 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), and select().
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Definition at line 306 of file ComputeNonbondedUtil.h.
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Definition at line 289 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), buildForceAndEnergyTable(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::launchWork(), and select().
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Definition at line 290 of file ComputeNonbondedUtil.h.
Referenced by ExclElem::computeForce(), ComputeNonbondedCUDA::doWork(), ComputeNonbondedCUDA::recvYieldDevice(), and select().
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Definition at line 291 of file ComputeNonbondedUtil.h.
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Definition at line 361 of file ComputeNonbondedUtil.h.
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Definition at line 367 of file ComputeNonbondedUtil.h.
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Definition at line 362 of file ComputeNonbondedUtil.h.
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Definition at line 368 of file ComputeNonbondedUtil.h.
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Definition at line 292 of file ComputeNonbondedUtil.h.
Referenced by ExclElem::computeForce(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), HomePatch::positionsReady(), and select().
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Definition at line 409 of file ComputeNonbondedUtil.h.
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Definition at line 412 of file ComputeNonbondedUtil.h.
Referenced by ComputeEwald::ComputeEwald(), ComputePme::doWork(), ComputePmeMgr::gridCalc2R(), CudaPmePencilXYZ::initializeDevice(), CudaPmePencilZ::initializeDevice(), PmeXPencil::pme_kspace(), and select().
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Definition at line 303 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), ExclElem::computeForce(), and select().
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Definition at line 287 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::doWork(), and select().
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Definition at line 307 of file ComputeNonbondedUtil.h.
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Definition at line 423 of file ComputeNonbondedUtil.h.
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Definition at line 394 of file ComputeNonbondedUtil.h.
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Definition at line 293 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_lj_table(), ExclElem::computeForce(), dumpbench(), and select().
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Definition at line 294 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_exclusions(), ComputeNonbondedCUDA::doWork(), ComputeNonbondedCUDA::finishWork(), and select().
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Definition at line 398 of file ComputeNonbondedUtil.h.
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Definition at line 399 of file ComputeNonbondedUtil.h.
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Definition at line 413 of file ComputeNonbondedUtil.h.
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Definition at line 403 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), select(), and submitPressureProfileData().
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Definition at line 405 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and ComputeNonbondedSelf::doForce().
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Definition at line 401 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::noWork(), ComputeNonbondedSelf::noWork(), and select().
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Definition at line 402 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), select(), and submitPressureProfileData().
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Definition at line 404 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedPair::doForce(), and ComputeNonbondedSelf::doForce().
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Definition at line 288 of file ComputeNonbondedUtil.h.
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Definition at line 295 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), buildForceAndEnergyTable(), ExclElem::computeForce(), and select().
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Definition at line 295 of file ComputeNonbondedUtil.h.
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Definition at line 298 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), buildForceAndEnergyTable(), ExclElem::computeForce(), and select().
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Definition at line 310 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), buildForceAndEnergyTable(), ExclElem::computeForce(), and select().
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Definition at line 296 of file ComputeNonbondedUtil.h.
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Definition at line 353 of file ComputeNonbondedUtil.h.
Referenced by ExclElem::computeForce(), and select().
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Definition at line 352 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_lj_table(), calcGBIS(), ExclElem::computeForce(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), HomePatch::positionsReady(), and select().
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Definition at line 304 of file ComputeNonbondedUtil.h.
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Definition at line 305 of file ComputeNonbondedUtil.h.
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Definition at line 308 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), and select().
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Definition at line 309 of file ComputeNonbondedUtil.h.
Referenced by ComputeNonbondedCUDA::build_force_table(), and select().
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Definition at line 389 of file ComputeNonbondedUtil.h.
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