| 50 |
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|
| 51 |
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namespace OpenMD { |
| 52 |
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|
| 53 |
< |
bool EAM::initialized_ = false; |
| 54 |
< |
RealType EAM::eamRcut_ = 0.0; |
| 55 |
< |
EAMMixingMethod EAM::mixMeth_ = eamJohnson; |
| 56 |
< |
ForceField* EAM::forceField_ = NULL; |
| 57 |
< |
map<int, AtomType*> EAM::EAMlist; |
| 58 |
< |
map<AtomType*, EAMAtomData> EAM::EAMMap; |
| 59 |
< |
map<pair<AtomType*, AtomType*>, EAMInteractionData> EAM::MixingMap; |
| 60 |
< |
|
| 61 |
< |
|
| 62 |
< |
EAM* EAM::_instance = NULL; |
| 63 |
< |
|
| 64 |
< |
EAM* EAM::Instance() { |
| 65 |
< |
if (!_instance) { |
| 66 |
< |
_instance = new EAM(); |
| 67 |
< |
} |
| 68 |
< |
return _instance; |
| 69 |
< |
} |
| 53 |
> |
EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), |
| 54 |
> |
mixMeth_(eamJohnson), eamRcut_(0.0) {} |
| 55 |
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|
| 56 |
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EAMParam EAM::getEAMParam(AtomType* atomType) { |
| 57 |
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|
| 177 |
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for (int i = 1; i < rvals.size(); i++ ) { |
| 178 |
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r = rvals[i]; |
| 179 |
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|
| 180 |
< |
// only use z(r) if we're inside this atoms cutoff radius, otherwise, we'll use zero for the charge. |
| 181 |
< |
// This effectively means that our phi grid goes out beyond the cutoff of the pair potential |
| 180 |
> |
// only use z(r) if we're inside this atom's cutoff radius, |
| 181 |
> |
// otherwise, we'll use zero for the charge. This effectively |
| 182 |
> |
// means that our phi grid goes out beyond the cutoff of the |
| 183 |
> |
// pair potential |
| 184 |
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|
| 185 |
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zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; |
| 186 |
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zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; |
| 347 |
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return; |
| 348 |
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} |
| 349 |
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|
| 350 |
< |
void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, |
| 364 |
< |
RealType &rho_i_at_j, RealType &rho_j_at_i) { |
| 350 |
> |
void EAM::calcDensity(InteractionData &idat) { |
| 351 |
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|
| 352 |
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if (!initialized_) initialize(); |
| 353 |
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|
| 354 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 355 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 354 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 355 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 356 |
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|
| 357 |
< |
if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij); |
| 358 |
< |
if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij); |
| 357 |
> |
if ( *(idat.rij) < data1.rcut) |
| 358 |
> |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 359 |
> |
|
| 360 |
> |
|
| 361 |
> |
if ( *(idat.rij) < data2.rcut) |
| 362 |
> |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 363 |
> |
|
| 364 |
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return; |
| 365 |
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} |
| 366 |
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|
| 367 |
< |
void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho, |
| 377 |
< |
RealType &dfrhodrho) { |
| 367 |
> |
void EAM::calcFunctional(SelfData &sdat) { |
| 368 |
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|
| 369 |
|
if (!initialized_) initialize(); |
| 370 |
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|
| 371 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 371 |
> |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 372 |
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|
| 373 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho); |
| 373 |
> |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 374 |
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|
| 375 |
< |
frho = result.first; |
| 376 |
< |
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 |
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return; |
| 382 |
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} |
| 383 |
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|
| 384 |
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|
| 385 |
< |
void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 392 |
< |
RealType rij, RealType r2, RealType sw, |
| 393 |
< |
RealType &vpair, RealType &pot, Vector3d &f1, |
| 394 |
< |
RealType rho_i, RealType rho_j, |
| 395 |
< |
RealType dfrhodrho_i, RealType dfrhodrho_j, |
| 396 |
< |
RealType &fshift_i, RealType &fshift_j) { |
| 385 |
> |
void EAM::calcForce(InteractionData &idat) { |
| 386 |
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|
| 387 |
|
if (!initialized_) initialize(); |
| 388 |
|
|
| 389 |
|
pair<RealType, RealType> res; |
| 390 |
|
|
| 391 |
< |
if (rij < eamRcut_) { |
| 391 |
> |
if ( *(idat.rij) < eamRcut_) { |
| 392 |
|
|
| 393 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 394 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 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 (rij < rci) { |
| 407 |
< |
res = data1.rho->getValueAndDerivativeAt(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(at1, at1)].phi->getValueAndDerivativeAt(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 (rij < rcj) { |
| 417 |
< |
res = data2.rho->getValueAndDerivativeAt(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(at2, at2)].phi->getValueAndDerivativeAt(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 |
|
} |
| 425 |
|
|
| 437 |
– |
phab = 0.0; |
| 438 |
– |
dvpdr = 0.0; |
| 439 |
– |
|
| 426 |
|
switch(mixMeth_) { |
| 427 |
|
case eamJohnson: |
| 428 |
|
|
| 429 |
< |
if (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 (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(at1,at2)].phi->getValueAndDerivativeAt(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*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr; |
| 466 |
> |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 467 |
|
|
| 468 |
< |
f1 = d * dudr / 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. |
| 490 |
< |
// |
| 491 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 492 |
< |
// pair interaction, and will be handled by vpair. |
| 493 |
< |
|
| 494 |
< |
fshift_i = data1.F->getValueAt( rho_i - rhb ); |
| 495 |
< |
fshift_j = data1.F->getValueAt( rho_j - 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 |
< |
pot += phab; |
| 479 |
> |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 480 |
> |
- *(idat.frho2); |
| 481 |
|
|
| 482 |
< |
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(pair<AtomType*, AtomType*> atypes) { |
| 495 |
+ |
if (!initialized_) initialize(); |
| 496 |
|
|
| 497 |
< |
void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij, |
| 508 |
< |
RealType* rho_i_at_j, RealType* rho_j_at_i){ |
| 497 |
> |
RealType cut = 0.0; |
| 498 |
|
|
| 499 |
< |
if (!initialized_) initialize(); |
| 511 |
< |
|
| 512 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 513 |
< |
AtomType* atype2 = EAMlist[*atid2]; |
| 514 |
< |
|
| 515 |
< |
calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
| 499 |
> |
map<AtomType*, EAMAtomData>::iterator it; |
| 500 |
|
|
| 501 |
< |
return; |
| 502 |
< |
} |
| 501 |
> |
it = EAMMap.find(atypes.first); |
| 502 |
> |
if (it != EAMMap.end()) { |
| 503 |
> |
EAMAtomData data1 = (*it).second; |
| 504 |
> |
cut = data1.rcut; |
| 505 |
> |
} |
| 506 |
|
|
| 507 |
< |
void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho, |
| 508 |
< |
RealType *dfrhodrho) { |
| 507 |
> |
it = EAMMap.find(atypes.second); |
| 508 |
> |
if (it != EAMMap.end()) { |
| 509 |
> |
EAMAtomData data2 = (*it).second; |
| 510 |
> |
if (data2.rcut > cut) |
| 511 |
> |
cut = data2.rcut; |
| 512 |
> |
} |
| 513 |
|
|
| 514 |
< |
if (!initialized_) initialize(); |
| 524 |
< |
|
| 525 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 526 |
< |
|
| 527 |
< |
calcFunctional(atype1, *rho, *frho, *dfrhodrho); |
| 528 |
< |
|
| 529 |
< |
return; |
| 514 |
> |
return cut; |
| 515 |
|
} |
| 531 |
– |
RealType EAM::getEAMcut(int *atid1) { |
| 532 |
– |
|
| 533 |
– |
if (!initialized_) initialize(); |
| 534 |
– |
|
| 535 |
– |
AtomType* atype1 = EAMlist[*atid1]; |
| 536 |
– |
|
| 537 |
– |
return getRcut(atype1); |
| 538 |
– |
} |
| 539 |
– |
|
| 540 |
– |
void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 541 |
– |
RealType *r2, RealType *sw, RealType *vpair, |
| 542 |
– |
RealType *pot, RealType *f1, RealType *rho1, |
| 543 |
– |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 544 |
– |
RealType *fshift1, RealType *fshift2) { |
| 545 |
– |
|
| 546 |
– |
if (!initialized_) initialize(); |
| 547 |
– |
|
| 548 |
– |
AtomType* atype1 = EAMlist[*atid1]; |
| 549 |
– |
AtomType* atype2 = EAMlist[*atid2]; |
| 550 |
– |
|
| 551 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 552 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 553 |
– |
|
| 554 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair, *pot, frc, |
| 555 |
– |
*rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2); |
| 556 |
– |
|
| 557 |
– |
f1[0] = frc.x(); |
| 558 |
– |
f1[1] = frc.y(); |
| 559 |
– |
f1[2] = frc.z(); |
| 560 |
– |
|
| 561 |
– |
return; |
| 562 |
– |
} |
| 563 |
– |
|
| 564 |
– |
void EAM::setCutoffEAM(RealType *thisRcut) { |
| 565 |
– |
eamRcut_ = *thisRcut; |
| 566 |
– |
} |
| 516 |
|
} |
| 517 |
|
|
| 569 |
– |
extern "C" { |
| 570 |
– |
|
| 571 |
– |
#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO) |
| 572 |
– |
#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO) |
| 573 |
– |
#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR) |
| 574 |
– |
#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM) |
| 575 |
– |
#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT) |
| 576 |
– |
|
| 577 |
– |
|
| 578 |
– |
void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, |
| 579 |
– |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 580 |
– |
|
| 581 |
– |
return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij, |
| 582 |
– |
rho_i_at_j, |
| 583 |
– |
rho_j_at_i); |
| 584 |
– |
} |
| 585 |
– |
void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, |
| 586 |
– |
RealType *dfrhodrho) { |
| 587 |
– |
|
| 588 |
– |
return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho, |
| 589 |
– |
dfrhodrho); |
| 590 |
– |
|
| 591 |
– |
} |
| 592 |
– |
void fortranSetCutoffEAM(RealType *rcut) { |
| 593 |
– |
return OpenMD::EAM::Instance()->setCutoffEAM(rcut); |
| 594 |
– |
} |
| 595 |
– |
void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 596 |
– |
RealType *r2, RealType *sw, RealType *vpair, |
| 597 |
– |
RealType *pot, RealType *f1, RealType *rho1, |
| 598 |
– |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 599 |
– |
RealType *fshift1, RealType *fshift2){ |
| 600 |
– |
|
| 601 |
– |
return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij, |
| 602 |
– |
r2, sw, vpair, |
| 603 |
– |
pot, f1, rho1, |
| 604 |
– |
rho2, dfrho1, dfrho2, |
| 605 |
– |
fshift1, fshift2); |
| 606 |
– |
} |
| 607 |
– |
RealType fortranGetEAMcut(int* atid) { |
| 608 |
– |
return OpenMD::EAM::Instance()->getEAMcut(atid); |
| 609 |
– |
} |
| 610 |
– |
|
| 611 |
– |
} |
