| 347 |
|
return; |
| 348 |
|
} |
| 349 |
|
|
| 350 |
< |
void EAM::calcDensity(DensityData ddat) { |
| 350 |
> |
void EAM::calcDensity(InteractionData &idat) { |
| 351 |
|
|
| 352 |
|
if (!initialized_) initialize(); |
| 353 |
|
|
| 354 |
< |
EAMAtomData data1 = EAMMap[ddat.atype1]; |
| 355 |
< |
EAMAtomData data2 = EAMMap[ddat.atype2]; |
| 354 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 355 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 356 |
|
|
| 357 |
< |
if (ddat.rij < data1.rcut) |
| 358 |
< |
ddat.rho_i_at_j = data1.rho->getValueAt(ddat.rij); |
| 357 |
> |
if ( *(idat.rij) < data1.rcut) |
| 358 |
> |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 359 |
|
|
| 360 |
– |
if (ddat.rij < data2.rcut) |
| 361 |
– |
ddat.rho_j_at_i = data2.rho->getValueAt(ddat.rij); |
| 360 |
|
|
| 361 |
+ |
if ( *(idat.rij) < data2.rcut) |
| 362 |
+ |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 363 |
+ |
|
| 364 |
|
return; |
| 365 |
|
} |
| 366 |
|
|
| 367 |
< |
void EAM::calcFunctional(FunctionalData fdat) { |
| 367 |
> |
void EAM::calcFunctional(SelfData &sdat) { |
| 368 |
|
|
| 369 |
|
if (!initialized_) initialize(); |
| 370 |
|
|
| 371 |
< |
EAMAtomData data1 = EAMMap[fdat.atype]; |
| 371 |
> |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 372 |
|
|
| 373 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(fdat.rho); |
| 373 |
> |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 374 |
|
|
| 375 |
< |
fdat.frho = result.first; |
| 376 |
< |
fdat.dfrhodrho = result.second; |
| 375 |
> |
*(sdat.frho) = result.first; |
| 376 |
> |
*(sdat.dfrhodrho) = result.second; |
| 377 |
> |
|
| 378 |
> |
sdat.pot[METALLIC_FAMILY] += result.first; |
| 379 |
> |
*(sdat.particlePot) += result.first; |
| 380 |
> |
|
| 381 |
|
return; |
| 382 |
|
} |
| 383 |
|
|
| 384 |
|
|
| 385 |
< |
void EAM::calcForce(InteractionData idat) { |
| 385 |
> |
void EAM::calcForce(InteractionData &idat) { |
| 386 |
|
|
| 387 |
|
if (!initialized_) initialize(); |
| 388 |
|
|
| 389 |
|
pair<RealType, RealType> res; |
| 390 |
|
|
| 391 |
< |
if (idat.rij < eamRcut_) { |
| 391 |
> |
if ( *(idat.rij) < eamRcut_) { |
| 392 |
|
|
| 393 |
< |
EAMAtomData data1 = EAMMap[idat.atype1]; |
| 394 |
< |
EAMAtomData data2 = EAMMap[idat.atype2]; |
| 393 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 394 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 395 |
|
|
| 396 |
|
// get type-specific cutoff radii |
| 397 |
|
|
| 398 |
|
RealType rci = data1.rcut; |
| 399 |
|
RealType rcj = data2.rcut; |
| 400 |
|
|
| 401 |
< |
RealType rha, drha, rhb, drhb; |
| 402 |
< |
RealType pha, dpha, phb, dphb; |
| 403 |
< |
RealType phab, dvpdr; |
| 401 |
> |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 402 |
> |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 403 |
> |
RealType phab(0.0), dvpdr(0.0); |
| 404 |
|
RealType drhoidr, drhojdr, dudr; |
| 405 |
|
|
| 406 |
< |
if (idat.rij < rci) { |
| 407 |
< |
res = data1.rho->getValueAndDerivativeAt(idat.rij); |
| 406 |
> |
if ( *(idat.rij) < rci) { |
| 407 |
> |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 408 |
|
rha = res.first; |
| 409 |
|
drha = res.second; |
| 410 |
|
|
| 411 |
< |
res = MixingMap[make_pair(idat.atype1, idat.atype1)].phi->getValueAndDerivativeAt(idat.rij); |
| 411 |
> |
res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 412 |
|
pha = res.first; |
| 413 |
|
dpha = res.second; |
| 414 |
|
} |
| 415 |
|
|
| 416 |
< |
if (idat.rij < rcj) { |
| 417 |
< |
res = data2.rho->getValueAndDerivativeAt(idat.rij); |
| 416 |
> |
if ( *(idat.rij) < rcj) { |
| 417 |
> |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 418 |
|
rhb = res.first; |
| 419 |
|
drhb = res.second; |
| 420 |
|
|
| 421 |
< |
res = MixingMap[make_pair(idat.atype2, idat.atype2)].phi->getValueAndDerivativeAt(idat.rij); |
| 421 |
> |
res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 422 |
|
phb = res.first; |
| 423 |
|
dphb = res.second; |
| 424 |
|
} |
| 420 |
– |
|
| 421 |
– |
phab = 0.0; |
| 422 |
– |
dvpdr = 0.0; |
| 425 |
|
|
| 426 |
|
switch(mixMeth_) { |
| 427 |
|
case eamJohnson: |
| 428 |
|
|
| 429 |
< |
if (idat.rij < rci) { |
| 429 |
> |
if ( *(idat.rij) < rci) { |
| 430 |
|
phab = phab + 0.5 * (rhb / rha) * pha; |
| 431 |
|
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 432 |
|
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 433 |
|
} |
| 434 |
+ |
|
| 435 |
+ |
|
| 436 |
|
|
| 437 |
< |
if (idat.rij < rcj) { |
| 437 |
> |
if ( *(idat.rij) < rcj) { |
| 438 |
|
phab = phab + 0.5 * (rha / rhb) * phb; |
| 439 |
|
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 440 |
|
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 443 |
|
break; |
| 444 |
|
|
| 445 |
|
case eamDaw: |
| 446 |
< |
res = MixingMap[make_pair(idat.atype1,idat.atype2)].phi->getValueAndDerivativeAt(idat.rij); |
| 446 |
> |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 447 |
|
phab = res.first; |
| 448 |
|
dvpdr = res.second; |
| 449 |
|
|
| 463 |
|
drhoidr = drha; |
| 464 |
|
drhojdr = drhb; |
| 465 |
|
|
| 466 |
< |
dudr = drhojdr*idat.dfrho1 + drhoidr*idat.dfrho2 + dvpdr; |
| 466 |
> |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 467 |
|
|
| 468 |
< |
idat.f1 = idat.d * dudr / idat.rij; |
| 468 |
> |
*(idat.f1) = *(idat.d) * dudr / *(idat.rij); |
| 469 |
|
|
| 470 |
< |
// particle_pot is the difference between the full potential |
| 471 |
< |
// and the full potential without the presence of a particular |
| 470 |
> |
// particlePot is the difference between the full potential and |
| 471 |
> |
// the full potential without the presence of a particular |
| 472 |
|
// particle (atom1). |
| 473 |
|
// |
| 474 |
< |
// This reduces the density at other particle locations, so |
| 475 |
< |
// we need to recompute the density at atom2 assuming atom1 |
| 476 |
< |
// didn't contribute. This then requires recomputing the |
| 477 |
< |
// density functional for atom2 as well. |
| 474 |
< |
// |
| 475 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 476 |
< |
// pair interaction, and will be handled by vpair. |
| 477 |
< |
|
| 478 |
< |
idat.fshift1 = data1.F->getValueAt( idat.rho1 - rhb ); |
| 479 |
< |
idat.fshift2 = data1.F->getValueAt( idat.rho2 - rha ); |
| 474 |
> |
// This reduces the density at other particle locations, so we |
| 475 |
> |
// need to recompute the density at atom2 assuming atom1 didn't |
| 476 |
> |
// contribute. This then requires recomputing the density |
| 477 |
> |
// functional for atom2 as well. |
| 478 |
|
|
| 479 |
< |
idat.pot += phab; |
| 479 |
> |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 480 |
> |
- *(idat.frho2); |
| 481 |
|
|
| 482 |
< |
idat.vpair += phab; |
| 482 |
> |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 483 |
> |
- *(idat.frho1); |
| 484 |
> |
|
| 485 |
> |
idat.pot[METALLIC_FAMILY] += phab; |
| 486 |
> |
|
| 487 |
> |
*(idat.vpair) += phab; |
| 488 |
|
} |
| 489 |
|
|
| 490 |
|
return; |
| 491 |
|
|
| 492 |
|
} |
| 493 |
|
|
| 494 |
< |
RealType EAM::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 494 |
> |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 495 |
|
if (!initialized_) initialize(); |
| 496 |
|
|
| 497 |
|
RealType cut = 0.0; |
| 498 |
|
|
| 499 |
|
map<AtomType*, EAMAtomData>::iterator it; |
| 500 |
|
|
| 501 |
< |
it = EAMMap.find(at1); |
| 501 |
> |
it = EAMMap.find(atypes.first); |
| 502 |
|
if (it != EAMMap.end()) { |
| 503 |
|
EAMAtomData data1 = (*it).second; |
| 504 |
|
cut = data1.rcut; |
| 505 |
|
} |
| 506 |
|
|
| 507 |
< |
it = EAMMap.find(at2); |
| 507 |
> |
it = EAMMap.find(atypes.second); |
| 508 |
|
if (it != EAMMap.end()) { |
| 509 |
|
EAMAtomData data2 = (*it).second; |
| 510 |
|
if (data2.rcut > cut) |
