#include <ComputeNonbondedUtil.h>
Inheritance diagram for ComputeNonbondedUtil:
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Definition at line 175 of file ComputeNonbondedUtil.h. 00175 { exclChecksumIndex, pairlistWarningIndex,
00176 electEnergyIndex, fullElectEnergyIndex, vdwEnergyIndex,
00177 //sd-db
00178 electEnergyIndex_s, fullElectEnergyIndex_s, vdwEnergyIndex_s,
00179 electEnergyIndex_ti_1, fullElectEnergyIndex_ti_1, vdwEnergyIndex_ti_1,
00180 electEnergyIndex_ti_2, fullElectEnergyIndex_ti_2, vdwEnergyIndex_ti_2,
00181 //sd-de
00182 TENSOR(virialIndex), TENSOR(fullElectVirialIndex),
00183 VECTOR(pairVDWForceIndex), VECTOR(pairElectForceIndex),
00184 reductionDataSize };
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Definition at line 151 of file ComputeNonbondedUtil.h. 00151 {}
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Definition at line 152 of file ComputeNonbondedUtil.h. 00152 {}
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Definition at line 180 of file ComputeNonbondedUtil.C. References NAMD_bug(). 00180 {
00181 NAMD_bug("Tried to call missing nonbonded compute routine.");
00182 }
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Definition at line 184 of file ComputeNonbondedUtil.C. References SimParameters::alchDecouple, alchDecouple, SimParameters::alchElecLambdaStart, alchElecLambdaStart, SimParameters::alchFepOn, alchFepOn, SimParameters::alchLambda, alchLambda, SimParameters::alchLambda2, alchLambda2, SimParameters::alchThermIntOn, alchThermIntOn, SimParameters::alchVdwLambdaEnd, alchVdwLambdaEnd, SimParameters::alchVdwShiftCoeff, alchVdwShiftCoeff, BigReal, Bool, build_cuda_force_table(), c0, C1, c1, C2, c3, c5, c6, c7, c8, calcFullPair, calcFullPairEnergy, calcFullSelf, calcFullSelfEnergy, calcMergePair, calcMergePairEnergy, calcMergeSelf, calcMergeSelfEnergy, calcPair, calcPairEnergy, calcSelf, calcSelfEnergy, calcSlowPair, calcSlowPairEnergy, calcSlowSelf, calcSlowSelfEnergy, Parameters::columnsize, columnsize, SimParameters::commOnly, commOnly, corr_table, SimParameters::cutoff, cutoff, cutoff2, SimParameters::dielectric, dielectric_1, ewaldcof, SimParameters::exclude, fast_table, SimParameters::fixedAtomsForces, SimParameters::fixedAtomsOn, fixedAtomsOn, SimParameters::FMAOn, full_table, SimParameters::fullDirectOn, iINFO(), iout, j, lambda_table, SimParameters::lesFactor, lesFactor, SimParameters::lesOn, lesOn, lesScaling, SimParameters::limitDist, ljTable, SimParameters::longSplitting, mol, Node::molecule, NAMD_bug(), NAMD_die(), SimParameters::nonbondedScaling, Node::Object(), SimParameters::pairInteractionOn, pairInteractionOn, SimParameters::pairInteractionSelf, pairInteractionSelf, Node::parameters, pi_ewaldcof, SimParameters::PMEEwaldCoefficient, SimParameters::PMEOn, SimParameters::pressureProfileAtomTypes, pressureProfileAtomTypes, SimParameters::pressureProfileOn, pressureProfileOn, SimParameters::pressureProfileSlabs, pressureProfileSlabs, r2_delta, r2_delta_1, r2_delta_exp, r2_table, Parameters::rowsize, rowsize, SimParameters::scale14, scale14, scaling, scor_table, SHARP, Node::simParameters, simParams, slow_table, SPLIT_C1, SPLIT_C2, SPLIT_NONE, SPLIT_SHIFT, SimParameters::switchingActive, SimParameters::switchingDist, switchOn, switchOn2, switchOn_1, table_alloc, Parameters::table_ener, table_ener, table_noshort, table_short, SimParameters::tabulatedEnergies, vdwa_table, vdwb_table, and XPLOR. Referenced by ComputeMgr::createComputes(), and SimParameters::scriptSet(). 00185 {
00186 if ( CkMyRank() ) return;
00187
00188 // These defaults die cleanly if nothing appropriate is assigned.
00189 ComputeNonbondedUtil::calcPair = calc_error;
00190 ComputeNonbondedUtil::calcPairEnergy = calc_error;
00191 ComputeNonbondedUtil::calcSelf = calc_error;
00192 ComputeNonbondedUtil::calcSelfEnergy = calc_error;
00193 ComputeNonbondedUtil::calcFullPair = calc_error;
00194 ComputeNonbondedUtil::calcFullPairEnergy = calc_error;
00195 ComputeNonbondedUtil::calcFullSelf = calc_error;
00196 ComputeNonbondedUtil::calcFullSelfEnergy = calc_error;
00197 ComputeNonbondedUtil::calcMergePair = calc_error;
00198 ComputeNonbondedUtil::calcMergePairEnergy = calc_error;
00199 ComputeNonbondedUtil::calcMergeSelf = calc_error;
00200 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_error;
00201 ComputeNonbondedUtil::calcSlowPair = calc_error;
00202 ComputeNonbondedUtil::calcSlowPairEnergy = calc_error;
00203 ComputeNonbondedUtil::calcSlowSelf = calc_error;
00204 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_error;
00205
00206 SimParameters * simParams = Node::Object()->simParameters;
00207 Parameters * params = Node::Object()->parameters;
00208
00209 table_ener = params->table_ener;
00210 rowsize = params->rowsize;
00211 columnsize = params->columnsize;
00212
00213 commOnly = simParams->commOnly;
00214 fixedAtomsOn = ( simParams->fixedAtomsOn && ! simParams->fixedAtomsForces );
00215
00216 cutoff = simParams->cutoff;
00217 cutoff2 = cutoff*cutoff;
00218
00219 //fepb
00220 alchFepOn = simParams->alchFepOn;
00221 alchThermIntOn = simParams->alchThermIntOn;
00222 alchLambda = alchLambda2 = 0;
00223 lesOn = simParams->lesOn;
00224 lesScaling = lesFactor = 0;
00225 Bool tabulatedEnergies = simParams->tabulatedEnergies;
00226 alchVdwShiftCoeff = simParams->alchVdwShiftCoeff;
00227 alchVdwLambdaEnd = simParams->alchVdwLambdaEnd;
00228 alchElecLambdaStart = simParams->alchElecLambdaStart;
00229
00230 alchDecouple = simParams->alchDecouple;
00231
00232 delete [] lambda_table;
00233 lambda_table = 0;
00234
00235 pairInteractionOn = simParams->pairInteractionOn;
00236 pairInteractionSelf = simParams->pairInteractionSelf;
00237 pressureProfileOn = simParams->pressureProfileOn;
00238
00239 if ( alchFepOn ) {
00240 alchLambda = simParams->alchLambda;
00241 alchLambda2 = simParams->alchLambda2;
00242 ComputeNonbondedUtil::calcPair = calc_pair_energy_fep;
00243 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_fep;
00244 ComputeNonbondedUtil::calcSelf = calc_self_energy_fep;
00245 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_fep;
00246 ComputeNonbondedUtil::calcFullPair = calc_pair_energy_fullelect_fep;
00247 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_fep;
00248 ComputeNonbondedUtil::calcFullSelf = calc_self_energy_fullelect_fep;
00249 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_fep;
00250 ComputeNonbondedUtil::calcMergePair = calc_pair_energy_merge_fullelect_fep;
00251 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_fep;
00252 ComputeNonbondedUtil::calcMergeSelf = calc_self_energy_merge_fullelect_fep;
00253 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_fep;
00254 ComputeNonbondedUtil::calcSlowPair = calc_pair_energy_slow_fullelect_fep;
00255 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect_fep;
00256 ComputeNonbondedUtil::calcSlowSelf = calc_self_energy_slow_fullelect_fep;
00257 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect_fep;
00258 } else if ( alchThermIntOn ) {
00259 alchLambda = simParams->alchLambda;
00260 ComputeNonbondedUtil::calcPair = calc_pair_ti;
00261 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_ti;
00262 ComputeNonbondedUtil::calcSelf = calc_self_ti;
00263 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_ti;
00264 ComputeNonbondedUtil::calcFullPair = calc_pair_fullelect_ti;
00265 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_ti;
00266 ComputeNonbondedUtil::calcFullSelf = calc_self_fullelect_ti;
00267 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_ti;
00268 ComputeNonbondedUtil::calcMergePair = calc_pair_merge_fullelect_ti;
00269 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_ti;
00270 ComputeNonbondedUtil::calcMergeSelf = calc_self_merge_fullelect_ti;
00271 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_ti;
00272 ComputeNonbondedUtil::calcSlowPair = calc_pair_slow_fullelect_ti;
00273 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect_ti;
00274 ComputeNonbondedUtil::calcSlowSelf = calc_self_slow_fullelect_ti;
00275 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect_ti;
00276 } else if ( lesOn ) {
00277 lesFactor = simParams->lesFactor;
00278 lesScaling = 1.0 / (double)lesFactor;
00279 lambda_table = new BigReal[(lesFactor+1)*(lesFactor+1)];
00280 for ( int ip=0; ip<=lesFactor; ++ip ) {
00281 for ( int jp=0; jp<=lesFactor; ++jp ) {
00282 BigReal lambda_pair = 1.0;
00283 if (ip || jp ) {
00284 if (ip && jp && ip != jp) {
00285 lambda_pair = 0.0;
00286 } else {
00287 lambda_pair = lesScaling;
00288 }
00289 }
00290 lambda_table[(lesFactor+1)*ip+jp] = lambda_pair;
00291 }
00292 }
00293 ComputeNonbondedUtil::calcPair = calc_pair_les;
00294 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_les;
00295 ComputeNonbondedUtil::calcSelf = calc_self_les;
00296 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_les;
00297 ComputeNonbondedUtil::calcFullPair = calc_pair_fullelect_les;
00298 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_les;
00299 ComputeNonbondedUtil::calcFullSelf = calc_self_fullelect_les;
00300 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_les;
00301 ComputeNonbondedUtil::calcMergePair = calc_pair_merge_fullelect_les;
00302 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_les;
00303 ComputeNonbondedUtil::calcMergeSelf = calc_self_merge_fullelect_les;
00304 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_les;
00305 ComputeNonbondedUtil::calcSlowPair = calc_pair_slow_fullelect_les;
00306 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect_les;
00307 ComputeNonbondedUtil::calcSlowSelf = calc_self_slow_fullelect_les;
00308 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect_les;
00309 } else if ( pressureProfileOn) {
00310 pressureProfileSlabs = simParams->pressureProfileSlabs;
00311 pressureProfileAtomTypes = simParams->pressureProfileAtomTypes;
00312
00313 ComputeNonbondedUtil::calcPair = calc_pair_pprof;
00314 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_pprof;
00315 ComputeNonbondedUtil::calcSelf = calc_self_pprof;
00316 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_pprof;
00317 ComputeNonbondedUtil::calcFullPair = calc_pair_fullelect_pprof;
00318 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_pprof;
00319 ComputeNonbondedUtil::calcFullSelf = calc_self_fullelect_pprof;
00320 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_pprof;
00321 ComputeNonbondedUtil::calcMergePair = calc_pair_merge_fullelect_pprof;
00322 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_pprof;
00323 ComputeNonbondedUtil::calcMergeSelf = calc_self_merge_fullelect_pprof;
00324 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_pprof;
00325 ComputeNonbondedUtil::calcSlowPair = calc_pair_slow_fullelect_pprof;
00326 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect_pprof;
00327 ComputeNonbondedUtil::calcSlowSelf = calc_self_slow_fullelect_pprof;
00328 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect_pprof;
00329 } else if ( pairInteractionOn ) {
00330 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_int;
00331 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_int;
00332 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_int;
00333 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_int;
00334 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_int;
00335 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_int;
00336 } else if ( tabulatedEnergies ) {
00337 ComputeNonbondedUtil::calcPair = calc_pair_tabener;
00338 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy_tabener;
00339 ComputeNonbondedUtil::calcSelf = calc_self_tabener;
00340 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy_tabener;
00341 ComputeNonbondedUtil::calcFullPair = calc_pair_fullelect_tabener;
00342 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect_tabener;
00343 ComputeNonbondedUtil::calcFullSelf = calc_self_fullelect_tabener;
00344 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect_tabener;
00345 ComputeNonbondedUtil::calcMergePair = calc_pair_merge_fullelect_tabener;
00346 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect_tabener;
00347 ComputeNonbondedUtil::calcMergeSelf = calc_self_merge_fullelect_tabener;
00348 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect_tabener;
00349 ComputeNonbondedUtil::calcSlowPair = calc_pair_slow_fullelect_tabener;
00350 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect_tabener;
00351 ComputeNonbondedUtil::calcSlowSelf = calc_self_slow_fullelect_tabener;
00352 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect_tabener;
00353 } else {
00354 ComputeNonbondedUtil::calcPair = calc_pair;
00355 ComputeNonbondedUtil::calcPairEnergy = calc_pair_energy;
00356 ComputeNonbondedUtil::calcSelf = calc_self;
00357 ComputeNonbondedUtil::calcSelfEnergy = calc_self_energy;
00358 ComputeNonbondedUtil::calcFullPair = calc_pair_fullelect;
00359 ComputeNonbondedUtil::calcFullPairEnergy = calc_pair_energy_fullelect;
00360 ComputeNonbondedUtil::calcFullSelf = calc_self_fullelect;
00361 ComputeNonbondedUtil::calcFullSelfEnergy = calc_self_energy_fullelect;
00362 ComputeNonbondedUtil::calcMergePair = calc_pair_merge_fullelect;
00363 ComputeNonbondedUtil::calcMergePairEnergy = calc_pair_energy_merge_fullelect;
00364 ComputeNonbondedUtil::calcMergeSelf = calc_self_merge_fullelect;
00365 ComputeNonbondedUtil::calcMergeSelfEnergy = calc_self_energy_merge_fullelect;
00366 ComputeNonbondedUtil::calcSlowPair = calc_pair_slow_fullelect;
00367 ComputeNonbondedUtil::calcSlowPairEnergy = calc_pair_energy_slow_fullelect;
00368 ComputeNonbondedUtil::calcSlowSelf = calc_self_slow_fullelect;
00369 ComputeNonbondedUtil::calcSlowSelfEnergy = calc_self_energy_slow_fullelect;
00370 }
00371
00372 //fepe
00373
00374 dielectric_1 = 1.0/simParams->dielectric;
00375 if ( ! ljTable ) ljTable = new LJTable;
00376 mol = Node::Object()->molecule;
00377 scaling = simParams->nonbondedScaling;
00378 if ( simParams->exclude == SCALED14 )
00379 {
00380 scale14 = simParams->scale14;
00381 }
00382 else
00383 {
00384 scale14 = 1.;
00385 }
00386 if ( simParams->switchingActive )
00387 {
00388 switchOn = simParams->switchingDist;
00389 switchOn_1 = 1.0/switchOn;
00390 // d0 = 1.0/(cutoff-switchOn);
00391 switchOn2 = switchOn*switchOn;
00392 c0 = 1.0/(cutoff2-switchOn2);
00393 }
00394 else
00395 {
00396 switchOn = cutoff;
00397 switchOn_1 = 1.0/switchOn;
00398 // d0 = 0.; // avoid division by zero
00399 switchOn2 = switchOn*switchOn;
00400 c0 = 0.; // avoid division by zero
00401 }
00402 c1 = c0*c0*c0;
00403 c3 = 3.0 * (cutoff2 - switchOn2);
00404 c5 = 0;
00405 c6 = 0;
00406 c7 = 0;
00407 c8 = 0;
00408
00409 const int PMEOn = simParams->PMEOn;
00410
00411 if ( PMEOn ) {
00412 ewaldcof = simParams->PMEEwaldCoefficient;
00413 BigReal TwoBySqrtPi = 1.12837916709551;
00414 pi_ewaldcof = TwoBySqrtPi * ewaldcof;
00415 }
00416
00417 int splitType = SPLIT_NONE;
00418 if ( simParams->switchingActive ) splitType = SPLIT_SHIFT;
00419 if ( simParams->fullDirectOn || simParams->FMAOn || PMEOn ) {
00420 switch ( simParams->longSplitting ) {
00421 case C2:
00422 splitType = SPLIT_C2;
00423 break;
00424
00425 case C1:
00426 splitType = SPLIT_C1;
00427 break;
00428
00429 case XPLOR:
00430 NAMD_die("Sorry, XPLOR splitting not supported.");
00431 break;
00432
00433 case SHARP:
00434 NAMD_die("Sorry, SHARP splitting not supported.");
00435 break;
00436
00437 default:
00438 NAMD_die("Unknown splitting type found!");
00439
00440 }
00441 }
00442
00443 BigReal r2_tol = 0.1;
00444
00445 r2_delta = 1.0;
00446 r2_delta_exp = 0;
00447 while ( r2_delta > r2_tol ) { r2_delta /= 2.0; r2_delta_exp += 1; }
00448 r2_delta_1 = 1.0 / r2_delta;
00449
00450 if ( ! CkMyPe() ) {
00451 iout << iINFO << "NONBONDED TABLE R-SQUARED SPACING: " <<
00452 r2_delta << "\n" << endi;
00453 }
00454
00455 BigReal r2_tmp = 1.0;
00456 int cutoff2_exp = 0;
00457 while ( (cutoff2 + r2_delta) > r2_tmp ) { r2_tmp *= 2.0; cutoff2_exp += 1; }
00458
00459 int i;
00460 int n = (r2_delta_exp + cutoff2_exp) * 64 + 1;
00461
00462 if ( ! CkMyPe() ) {
00463 iout << iINFO << "NONBONDED TABLE SIZE: " <<
00464 n << " POINTS\n" << endi;
00465 }
00466
00467 if ( table_alloc ) delete [] table_alloc;
00468 table_alloc = new BigReal[61*n+16];
00469 BigReal *table_align = table_alloc;
00470 while ( ((long)table_align) % 128 ) ++table_align;
00471 table_noshort = table_align;
00472 table_short = table_align + 16*n;
00473 slow_table = table_align + 32*n;
00474 fast_table = table_align + 36*n;
00475 scor_table = table_align + 40*n;
00476 corr_table = table_align + 44*n;
00477 full_table = table_align + 48*n;
00478 vdwa_table = table_align + 52*n;
00479 vdwb_table = table_align + 56*n;
00480 r2_table = table_align + 60*n;
00481 BigReal *fast_i = fast_table + 4;
00482 BigReal *scor_i = scor_table + 4;
00483 BigReal *slow_i = slow_table + 4;
00484 BigReal *vdwa_i = vdwa_table + 4;
00485 BigReal *vdwb_i = vdwb_table + 4;
00486 BigReal *r2_i = r2_table; *(r2_i++) = r2_delta;
00487 BigReal r2_limit = simParams->limitDist * simParams->limitDist;
00488 if ( r2_limit < r2_delta ) r2_limit = r2_delta;
00489 int r2_delta_i = 0; // entry for r2 == r2_delta
00490
00491 // fill in the table, fix up i==0 (r2==0) below
00492 for ( i=1; i<n; ++i ) {
00493
00494 const BigReal r2_base = r2_delta * ( 1 << (i/64) );
00495 const BigReal r2_del = r2_base / 64.0;
00496 const BigReal r2 = r2_base - r2_delta + r2_del * (i%64);
00497
00498 if ( r2 <= r2_limit ) r2_delta_i = i;
00499
00500 const BigReal r = sqrt(r2);
00501 const BigReal r_1 = 1.0/r;
00502 const BigReal r_2 = 1.0/r2;
00503
00504 // fast_ is defined as (full_ - slow_)
00505 // corr_ and fast_ are both zero at the cutoff, full_ is not
00506 // all three are approx 1/r at short distances
00507
00508 // for actual interpolation, we use fast_ for fast forces and
00509 // scor_ = slow_ + corr_ - full_ and slow_ for slow forces
00510 // since these last two are of small magnitude
00511
00512 BigReal fast_energy, fast_gradient;
00513 BigReal scor_energy, scor_gradient;
00514 BigReal slow_energy, slow_gradient;
00515
00516 // corr_ is PME direct sum, or similar correction term
00517 // corr_energy is multiplied by r until later
00518 // corr_gradient is multiplied by -r^2 until later
00519 BigReal corr_energy, corr_gradient;
00520
00521
00522 if ( PMEOn ) {
00523 BigReal tmp_a = r * ewaldcof;
00524 BigReal tmp_b = erfc(tmp_a);
00525 corr_energy = tmp_b;
00526 corr_gradient = pi_ewaldcof*exp(-(tmp_a*tmp_a))*r + tmp_b;
00527 } else {
00528 corr_energy = corr_gradient = 0;
00529 }
00530
00531 switch(splitType) {
00532 case SPLIT_NONE:
00533 fast_energy = 1.0/r;
00534 fast_gradient = -1.0/r2;
00535 scor_energy = scor_gradient = 0;
00536 slow_energy = slow_gradient = 0;
00537 break;
00538 case SPLIT_SHIFT: {
00539 BigReal shiftVal = r2/cutoff2 - 1.0;
00540 shiftVal *= shiftVal;
00541 BigReal dShiftVal = 2.0 * (r2/cutoff2 - 1.0) * 2.0*r/cutoff2;
00542 fast_energy = shiftVal/r;
00543 fast_gradient = dShiftVal/r - shiftVal/r2;
00544 scor_energy = scor_gradient = 0;
00545 slow_energy = slow_gradient = 0;
00546 }
00547 break;
00548 case SPLIT_C1:
00549 // calculate actual energy and gradient
00550 slow_energy = 0.5/cutoff * (3.0 - (r2/cutoff2));
00551 slow_gradient = -1.0/cutoff2 * (r/cutoff);
00552 // calculate scor from slow and corr
00553 scor_energy = slow_energy + (corr_energy - 1.0)/r;
00554 scor_gradient = slow_gradient - (corr_gradient - 1.0)/r2;
00555 // calculate fast from slow
00556 fast_energy = 1.0/r - slow_energy;
00557 fast_gradient = -1.0/r2 - slow_gradient;
00558 break;
00559 case SPLIT_C2:
00560 //
00561 // Quintic splitting function contributed by
00562 // Bruce Berne, Ruhong Zhou, and Joe Morrone
00563 //
00564 // calculate actual energy and gradient
00565 slow_energy = r2/(cutoff*cutoff2) * (6.0 * (r2/cutoff2)
00566 - 15.0*(r/cutoff) + 10.0);
00567 slow_gradient = r/(cutoff*cutoff2) * (24.0 * (r2/cutoff2)
00568 - 45.0 *(r/cutoff) + 20.0);
00569 // calculate scor from slow and corr
00570 scor_energy = slow_energy + (corr_energy - 1.0)/r;
00571 scor_gradient = slow_gradient - (corr_gradient - 1.0)/r2;
00572 // calculate fast from slow
00573 fast_energy = 1.0/r - slow_energy;
00574 fast_gradient = -1.0/r2 - slow_gradient;
00575 break;
00576 }
00577
00578 // foo_gradient is calculated as ( d foo_energy / d r )
00579 // and now divided by 2r to get ( d foo_energy / d r2 )
00580
00581 fast_gradient *= 0.5 * r_1;
00582 scor_gradient *= 0.5 * r_1;
00583 slow_gradient *= 0.5 * r_1;
00584
00585 // let modf be 1 if excluded, 1-scale14 if modified, 0 otherwise,
00586 // add scor_ - modf * slow_ to slow terms and
00587 // add fast_ - modf * fast_ to fast terms.
00588
00589 BigReal vdwa_energy, vdwa_gradient;
00590 BigReal vdwb_energy, vdwb_gradient;
00591
00592 const BigReal r_6 = r_2*r_2*r_2;
00593 const BigReal r_12 = r_6*r_6;
00594
00595 // Lennard-Jones switching function
00596 const BigReal c2 = cutoff2-r2;
00597 const BigReal c4 = c2*(c3-2.0*c2);
00598 const BigReal switchVal = // used for Lennard-Jones
00599 ( r2 > switchOn2 ? c2*c4*c1 : 1.0 );
00600 const BigReal dSwitchVal = // d switchVal / d r2
00601 ( r2 > switchOn2 ? 2*c1*(c2*c2-c4) : 0.0 );
00602
00603 vdwa_energy = switchVal * r_12;
00604 vdwb_energy = switchVal * r_6;
00605
00606 vdwa_gradient = ( dSwitchVal - 6.0 * switchVal * r_2 ) * r_12;
00607 vdwb_gradient = ( dSwitchVal - 3.0 * switchVal * r_2 ) * r_6;
00608
00609
00610 *(fast_i++) = fast_energy;
00611 *(fast_i++) = fast_gradient;
00612 *(fast_i++) = 0;
00613 *(fast_i++) = 0;
00614 *(scor_i++) = scor_energy;
00615 *(scor_i++) = scor_gradient;
00616 *(scor_i++) = 0;
00617 *(scor_i++) = 0;
00618 *(slow_i++) = slow_energy;
00619 *(slow_i++) = slow_gradient;
00620 *(slow_i++) = 0;
00621 *(slow_i++) = 0;
00622 *(vdwa_i++) = vdwa_energy;
00623 *(vdwa_i++) = vdwa_gradient;
00624 *(vdwa_i++) = 0;
00625 *(vdwa_i++) = 0;
00626 *(vdwb_i++) = vdwb_energy;
00627 *(vdwb_i++) = vdwb_gradient;
00628 *(vdwb_i++) = 0;
00629 *(vdwb_i++) = 0;
00630 *(r2_i++) = r2 + r2_delta;
00631
00632 }
00633
00634 if ( ! r2_delta_i ) {
00635 NAMD_bug("Failed to find table entry for r2 == r2_limit\n");
00636 }
00637 if ( r2_table[r2_delta_i] > r2_limit + r2_delta ) {
00638 NAMD_bug("Found bad table entry for r2 == r2_limit\n");
00639 }
00640
00641 int j;
00642 const char *table_name = "XXXX";
00643 int smooth_short = 0;
00644 for ( j=0; j<5; ++j ) {
00645 BigReal *t0 = 0;
00646 switch (j) {
00647 case 0:
00648 t0 = fast_table;
00649 table_name = "FAST";
00650 smooth_short = 1;
00651 break;
00652 case 1:
00653 t0 = scor_table;
00654 table_name = "SCOR";
00655 smooth_short = 0;
00656 break;
00657 case 2:
00658 t0 = slow_table;
00659 table_name = "SLOW";
00660 smooth_short = 0;
00661 break;
00662 case 3:
00663 t0 = vdwa_table;
00664 table_name = "VDWA";
00665 smooth_short = 1;
00666 break;
00667 case 4:
00668 t0 = vdwb_table;
00669 table_name = "VDWB";
00670 smooth_short = 1;
00671 break;
00672 }
00673 // patch up data for i=0
00674 t0[0] = t0[4] - t0[5] * ( r2_delta / 64.0 ); // energy
00675 t0[1] = t0[5]; // gradient
00676 t0[2] = 0;
00677 t0[3] = 0;
00678 if ( smooth_short ) {
00679 BigReal energy0 = t0[4*r2_delta_i];
00680 BigReal gradient0 = t0[4*r2_delta_i+1];
00681 BigReal r20 = r2_table[r2_delta_i];
00682 t0[0] = energy0 - gradient0 * (r20 - r2_table[0]); // energy
00683 t0[1] = gradient0; // gradient
00684 }
00685 BigReal *t;
00686 for ( i=0,t=t0; i<(n-1); ++i,t+=4 ) {
00687 BigReal x = ( r2_delta * ( 1 << (i/64) ) ) / 64.0;
00688 if ( r2_table[i+1] != r2_table[i] + x ) {
00689 NAMD_bug("Bad table delta calculation.\n");
00690 }
00691 if ( smooth_short && i+1 < r2_delta_i ) {
00692 BigReal energy0 = t0[4*r2_delta_i];
00693 BigReal gradient0 = t0[4*r2_delta_i+1];
00694 BigReal r20 = r2_table[r2_delta_i];
00695 t[4] = energy0 - gradient0 * (r20 - r2_table[i+1]); // energy
00696 t[5] = gradient0; // gradient
00697 }
00698 BigReal v1 = t[0];
00699 BigReal g1 = t[1];
00700 BigReal v2 = t[4];
00701 BigReal g2 = t[5];
00702 // explicit formulas for v1 + g1 x + c x^2 + d x^3
00703 BigReal c = ( 3.0 * (v2 - v1) - x * (2.0 * g1 + g2) ) / ( x * x );
00704 BigReal d = ( -2.0 * (v2 - v1) + x * (g1 + g2) ) / ( x * x * x );
00705 // since v2 - v1 is imprecise, we refine c and d numerically
00706 // important because we need accurate forces (more than energies!)
00707 for ( int k=0; k < 2; ++k ) {
00708 BigReal dv = (v1 - v2) + ( ( d * x + c ) * x + g1 ) * x;
00709 BigReal dg = (g1 - g2) + ( 3.0 * d * x + 2.0 * c ) * x;
00710 c -= ( 3.0 * dv - x * dg ) / ( x * x );
00711 d -= ( -2.0 * dv + x * dg ) / ( x * x * x );
00712 }
00713 // store in the array;
00714 t[2] = c; t[3] = d;
00715 }
00716
00717 if ( ! CkMyPe() ) {
00718 BigReal dvmax = 0;
00719 BigReal dgmax = 0;
00720 BigReal dvmax_r = 0;
00721 BigReal dgmax_r = 0;
00722 BigReal fdvmax = 0;
00723 BigReal fdgmax = 0;
00724 BigReal fdvmax_r = 0;
00725 BigReal fdgmax_r = 0;
00726 for ( i=0,t=t0; i<(n-1); ++i,t+=4 ) {
00727 const BigReal r2_base = r2_delta * ( 1 << (i/64) );
00728 const BigReal r2_del = r2_base / 64.0;
00729 const BigReal r2 = r2_base - r2_delta + r2_del * (i%64);
00730 const BigReal r = sqrt(r2);
00731 BigReal x = r2_del;
00732 BigReal dv = ( ( t[3] * x + t[2] ) * x + t[1] ) * x + t[0] - t[4];
00733 BigReal dg = ( 3.0 * t[3] * x + 2.0 * t[2] ) * x + t[1] - t[5];
00734 if ( t[4] != 0. && fabs(dv/t[4]) > fdvmax ) {
00735 fdvmax = fabs(dv/t[4]); fdvmax_r = r;
00736 }
00737 if ( fabs(dv) > dvmax ) {
00738 dvmax = fabs(dv); dvmax_r = r;
00739 }
00740 if ( t[5] != 0. && fabs(dg/t[5]) > fdgmax ) {
00741 fdgmax = fabs(dg/t[5]); fdgmax_r = r;
00742 }
00743 if ( fabs(dg) > dgmax ) {
00744 dgmax = fabs(dg); dgmax_r = r;
00745 }
00746 #if 0
00747 if (dv != 0.) CkPrintf("TABLE %d ENERGY ERROR %g AT %g (%d)\n",j,dv,r,i);
00748 if (dg != 0.) CkPrintf("TABLE %d FORCE ERROR %g AT %g (%d)\n",j,dg,r,i);
00749 #endif
00750 }
00751 if ( dvmax != 0.0 ) {
00752 iout << iINFO << "ABSOLUTE IMPRECISION IN " << table_name <<
00753 " TABLE ENERGY: " << dvmax << " AT " << dvmax_r << "\n" << endi;
00754 }
00755 if ( fdvmax != 0.0 ) {
00756 iout << iINFO << "RELATIVE IMPRECISION IN " << table_name <<
00757 " TABLE ENERGY: " << fdvmax << " AT " << fdvmax_r << "\n" << endi;
00758 }
00759 if ( dgmax != 0.0 ) {
00760 iout << iINFO << "ABSOLUTE IMPRECISION IN " << table_name <<
00761 " TABLE FORCE: " << dgmax << " AT " << dgmax_r << "\n" << endi;
00762 }
00763 if ( fdgmax != 0.0 ) {
00764 iout << iINFO << "RELATIVE IMPRECISION IN " << table_name <<
00765 " TABLE FORCE: " << fdgmax << " AT " << fdgmax_r << "\n" << endi;
00766 }
00767 }
00768
00769 }
00770
00771 for ( i=0; i<4*n; ++i ) {
00772 corr_table[i] = fast_table[i] + scor_table[i];
00773 full_table[i] = fast_table[i] + slow_table[i];
00774 }
00775
00776 #if 0
00777 for ( i=0; i<n; ++i ) {
00778 for ( int j=0; j<4; ++j ) {
00779 table_short[16*i+6-2*j] = table_noshort[16*i+6-2*j] = vdwa_table[4*i+j];
00780 table_short[16*i+7-2*j] = table_noshort[16*i+7-2*j] = vdwb_table[4*i+j];
00781 table_short[16*i+8+3-j] = fast_table[4*i+j];
00782 table_short[16*i+12+3-j] = scor_table[4*i+j];
00783 table_noshort[16*i+8+3-j] = corr_table[4*i+j];
00784 table_noshort[16*i+12+3-j] = full_table[4*i+j];
00785 }
00786 }
00787 #endif
00788
00789 for ( i=0; i<n; ++i ) {
00790 table_short[16*i+ 0] = table_noshort[16*i+0] = -6.*vdwa_table[4*i+3];
00791 table_short[16*i+ 2] = table_noshort[16*i+2] = -6.*vdwb_table[4*i+3];
00792 table_short[16*i+ 4] = table_noshort[16*i+4] = -2.*vdwa_table[4*i+1];
00793 table_short[16*i+ 6] = table_noshort[16*i+6] = -2.*vdwb_table[4*i+1];
00794
00795 table_short[16*i+1] = table_noshort[16*i+1] = -4.*vdwa_table[4*i+2];
00796 table_short[16*i+3] = table_noshort[16*i+3] = -4.*vdwb_table[4*i+2];
00797 table_short[16*i+5] = table_noshort[16*i+5] = -1.*vdwa_table[4*i+0];
00798 table_short[16*i+7] = table_noshort[16*i+7] = -1.*vdwb_table[4*i+0];
00799
00800 table_short[16*i+8] = -6.*fast_table[4*i+3];
00801 table_short[16*i+9] = -4.*fast_table[4*i+2];
00802 table_short[16*i+10] = -2.*fast_table[4*i+1];
00803 table_short[16*i+11] = -1.*fast_table[4*i+0];
00804
00805 table_noshort[16*i+8] = -6.*corr_table[4*i+3];
00806 table_noshort[16*i+9] = -4.*corr_table[4*i+2];
00807 table_noshort[16*i+10] = -2.*corr_table[4*i+1];
00808 table_noshort[16*i+11] = -1.*corr_table[4*i+0];
00809
00810 table_short[16*i+12] = -6.*scor_table[4*i+3];
00811 table_short[16*i+13] = -4.*scor_table[4*i+2];
00812 table_short[16*i+14] = -2.*scor_table[4*i+1];
00813 table_short[16*i+15] = -1.*scor_table[4*i+0];
00814
00815 table_noshort[16*i+12] = -6.*full_table[4*i+3];
00816 table_noshort[16*i+13] = -4.*full_table[4*i+2];
00817 table_noshort[16*i+14] = -2.*full_table[4*i+1];
00818 table_noshort[16*i+15] = -1.*full_table[4*i+0];
00819 }
00820
00821 #if 0
00822 char fname[100];
00823 sprintf(fname,"/tmp/namd.table.pe%d.dat",CkMyPe());
00824 FILE *f = fopen(fname,"w");
00825 for ( i=0; i<(n-1); ++i ) {
00826 const BigReal r2_base = r2_delta * ( 1 << (i/64) );
00827 const BigReal r2_del = r2_base / 64.0;
00828 const BigReal r2 = r2_base - r2_delta + r2_del * (i%64);
00829 BigReal *t;
00830 if ( r2 + r2_delta != r2_table[i] ) fprintf(f,"r2 error! ");
00831 fprintf(f,"%g",r2);
00832 t = fast_table + 4*i;
00833 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00834 t = scor_table + 4*i;
00835 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00836 t = slow_table + 4*i;
00837 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00838 t = corr_table + 4*i;
00839 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00840 t = full_table + 4*i;
00841 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00842 t = vdwa_table + 4*i;
00843 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00844 t = vdwb_table + 4*i;
00845 fprintf(f," %g %g %g %g", t[0], t[1], t[2], t[3]);
00846 fprintf(f,"\n");
00847 }
00848 fclose(f);
00849 #endif
00850
00851 #ifdef NAMD_CUDA
00852 build_cuda_force_table();
00853 #endif
00854
00855 }
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Definition at line 254 of file ComputeNonbondedUtil.h. References BigReal. 00257 {
00258 return(x*x+y*y+z*z);
00259 }
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Definition at line 149 of file ComputeNonbondedUtil.C. References SubmitReduction::add(), BigReal, and j. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedPair::noWork(). 00151 {
00152 if (!reduction) return;
00153 int numAtomTypes = pressureProfileAtomTypes;
00154 // For ease of calculation we stored interactions between types
00155 // i and j in (ni+j). For efficiency now we coalesce the
00156 // cross interactions so that just i<=j are stored.
00157 const int arraysize = 3*pressureProfileSlabs;
00158 size_t nelems = arraysize*(numAtomTypes*(numAtomTypes+1))/2;
00159 BigReal *arr = new BigReal[nelems];
00160 memset(arr, 0, nelems*sizeof(BigReal));
00161
00162 int i, j;
00163 for (i=0; i<numAtomTypes; i++) {
00164 for (j=0; j<numAtomTypes; j++) {
00165 int ii=i;
00166 int jj=j;
00167 if (ii > jj) { int tmp=ii; ii=jj; jj=tmp; }
00168 const int reductionOffset = (ii*numAtomTypes - (ii*(ii+1))/2 + jj)*arraysize;
00169 for (int k=0; k<arraysize; k++) {
00170 arr[reductionOffset+k] += data[k];
00171 }
00172 data += arraysize;
00173 }
00174 }
00175 // copy into reduction
00176 reduction->add(nelems, arr);
00177 delete [] arr;
00178 }
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Reimplemented in ExclElem. Definition at line 123 of file ComputeNonbondedUtil.C. References ADD_TENSOR, ADD_VECTOR, fullElectVirialIndex, SubmitReduction::item(), pairElectForceIndex, pairVDWForceIndex, 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_LJ_ENERGY, REDUCTION_LJ_ENERGY_F, REDUCTION_LJ_ENERGY_TI_1, REDUCTION_LJ_ENERGY_TI_2, REDUCTION_PAIR_ELECT_FORCE, REDUCTION_PAIR_VDW_FORCE, REDUCTION_PAIRLIST_WARNINGS, REDUCTION_VIRIAL_NBOND, REDUCTION_VIRIAL_SLOW, and virialIndex. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedPair::noWork(). 00124 {
00125 reduction->item(REDUCTION_EXCLUSION_CHECKSUM) += data[exclChecksumIndex];
00126 reduction->item(REDUCTION_PAIRLIST_WARNINGS) += data[pairlistWarningIndex];
00127 reduction->item(REDUCTION_ELECT_ENERGY) += data[electEnergyIndex];
00128 reduction->item(REDUCTION_ELECT_ENERGY_SLOW) += data[fullElectEnergyIndex];
00129 reduction->item(REDUCTION_LJ_ENERGY) += data[vdwEnergyIndex];
00130 //fepb
00131 reduction->item(REDUCTION_ELECT_ENERGY_F) += data[electEnergyIndex_s];
00132 reduction->item(REDUCTION_ELECT_ENERGY_SLOW_F) += data[fullElectEnergyIndex_s];
00133 reduction->item(REDUCTION_LJ_ENERGY_F) += data[vdwEnergyIndex_s];
00134
00135 reduction->item(REDUCTION_ELECT_ENERGY_TI_1) += data[electEnergyIndex_ti_1];
00136 reduction->item(REDUCTION_ELECT_ENERGY_SLOW_TI_1) += data[fullElectEnergyIndex_ti_1];
00137 reduction->item(REDUCTION_LJ_ENERGY_TI_1) += data[vdwEnergyIndex_ti_1];
00138 reduction->item(REDUCTION_ELECT_ENERGY_TI_2) += data[electEnergyIndex_ti_2];
00139 reduction->item(REDUCTION_ELECT_ENERGY_SLOW_TI_2) += data[fullElectEnergyIndex_ti_2];
00140 reduction->item(REDUCTION_LJ_ENERGY_TI_2) += data[vdwEnergyIndex_ti_2];
00141 //fepe
00142 ADD_TENSOR(reduction,REDUCTION_VIRIAL_NBOND,data,virialIndex);
00143 ADD_TENSOR(reduction,REDUCTION_VIRIAL_SLOW,data,fullElectVirialIndex);
00144 ADD_VECTOR(reduction,REDUCTION_PAIR_VDW_FORCE,data,pairVDWForceIndex);
00145 ADD_VECTOR(reduction,REDUCTION_PAIR_ELECT_FORCE,data,pairElectForceIndex);
00146 reduction->item(REDUCTION_COMPUTE_CHECKSUM) += 1.;
00147 }
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Definition at line 76 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 75 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 69 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 71 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 72 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 70 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 74 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 73 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 60 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 61 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 62 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 63 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 64 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 65 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 66 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 101 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 102 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 103 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 104 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 106 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 107 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 108 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 109 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 96 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 97 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 98 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 99 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 111 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 112 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedPair::doForce(), and select(). |
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Definition at line 113 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 114 of file ComputeNonbondedUtil.C. Referenced by ComputeNonbondedSelf::doForce(), and select(). |
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Definition at line 42 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 31 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 50 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 33 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 34 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 35 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 93 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 47 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 32 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 51 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 82 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 79 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 78 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 80 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 36 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 37 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 84 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 85 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 94 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Reimplemented in ExclElem. Definition at line 89 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Reimplemented in ExclElem. Definition at line 91 of file ComputeNonbondedUtil.C. |
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Definition at line 87 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Reimplemented in ExclElem. Definition at line 88 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Reimplemented in ExclElem. Definition at line 90 of file ComputeNonbondedUtil.C. |
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Definition at line 38 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 39 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 40 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 54 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 41 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 56 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 55 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 48 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 49 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 57 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 59 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 58 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 43 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 44 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 46 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 45 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 52 of file ComputeNonbondedUtil.C. Referenced by select(). |
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Definition at line 53 of file ComputeNonbondedUtil.C. Referenced by select(). |
1.3.9.1