| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
| 42 |
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| 43 |
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#include <stdio.h> |
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return; |
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} |
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|
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< |
void SC::calcDensity(DensityData ddat) { |
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> |
void SC::calcDensity(InteractionData &idat) { |
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| 308 |
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if (!initialized_) initialize(); |
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|
| 310 |
< |
SCInteractionData mixer = MixingMap[make_pair(ddat.atype1, ddat.atype2)]; |
| 310 |
> |
SCInteractionData mixer = MixingMap[ idat.atypes ]; |
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RealType rcij = mixer.rCut; |
| 313 |
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|
| 314 |
< |
if (ddat.rij < rcij) { |
| 315 |
< |
ddat.rho_i_at_j = mixer.phi->getValueAt(ddat.rij); |
| 316 |
< |
ddat.rho_j_at_i = ddat.rho_i_at_j; |
| 317 |
< |
} else { |
| 318 |
< |
ddat.rho_i_at_j = 0.0; |
| 319 |
< |
ddat.rho_j_at_i = 0.0; |
| 319 |
< |
} |
| 320 |
< |
|
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> |
if ( *(idat.rij) < rcij) { |
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> |
RealType rho = mixer.phi->getValueAt( *(idat.rij) ); |
| 316 |
> |
*(idat.rho1) += rho; |
| 317 |
> |
*(idat.rho2) += rho; |
| 318 |
> |
} |
| 319 |
> |
|
| 320 |
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return; |
| 321 |
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} |
| 322 |
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|
| 323 |
< |
void SC::calcFunctional(FunctionalData fdat) { |
| 323 |
> |
void SC::calcFunctional(SelfData &sdat) { |
| 324 |
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if (!initialized_) initialize(); |
| 326 |
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|
| 327 |
< |
SCAtomData data1 = SCMap[fdat.atype]; |
| 328 |
< |
|
| 329 |
< |
fdat.frho = - data1.c * data1.epsilon * sqrt(fdat.rho); |
| 330 |
< |
fdat.dfrhodrho = 0.5 * fdat.frho / fdat.rho; |
| 327 |
> |
SCAtomData data1 = SCMap[sdat.atype]; |
| 328 |
> |
|
| 329 |
> |
RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) ); |
| 330 |
> |
*(sdat.frho) = u; |
| 331 |
> |
*(sdat.dfrhodrho) = 0.5 * *(sdat.frho) / *(sdat.rho); |
| 332 |
> |
|
| 333 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += u; |
| 334 |
> |
*(sdat.particlePot) += u; |
| 335 |
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| 336 |
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return; |
| 337 |
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} |
| 338 |
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|
| 339 |
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|
| 340 |
< |
void SC::calcForce(InteractionData idat) { |
| 340 |
> |
void SC::calcForce(InteractionData &idat) { |
| 341 |
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|
| 342 |
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if (!initialized_) initialize(); |
| 343 |
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|
| 344 |
< |
SCAtomData data1 = SCMap[idat.atype1]; |
| 345 |
< |
SCAtomData data2 = SCMap[idat.atype2]; |
| 344 |
> |
SCAtomData data1 = SCMap[idat.atypes.first]; |
| 345 |
> |
SCAtomData data2 = SCMap[idat.atypes.second]; |
| 346 |
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|
| 347 |
< |
SCInteractionData mixer = MixingMap[make_pair(idat.atype1, idat.atype2)]; |
| 347 |
> |
SCInteractionData mixer = MixingMap[idat.atypes]; |
| 348 |
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|
| 349 |
|
RealType rcij = mixer.rCut; |
| 350 |
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|
| 351 |
< |
if (idat.rij < rcij) { |
| 351 |
> |
if ( *(idat.rij) < rcij) { |
| 352 |
|
RealType vcij = mixer.vCut; |
| 353 |
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|
| 354 |
|
pair<RealType, RealType> res; |
| 355 |
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|
| 356 |
< |
res = mixer.phi->getValueAndDerivativeAt(idat.rij); |
| 356 |
> |
res = mixer.phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 357 |
|
RealType rhtmp = res.first; |
| 358 |
|
RealType drhodr = res.second; |
| 359 |
|
|
| 360 |
< |
res = mixer.V->getValueAndDerivativeAt(idat.rij); |
| 360 |
> |
res = mixer.V->getValueAndDerivativeAt( *(idat.rij) ); |
| 361 |
|
RealType vptmp = res.first; |
| 362 |
|
RealType dvpdr = res.second; |
| 363 |
|
|
| 364 |
|
RealType pot_temp = vptmp - vcij; |
| 365 |
< |
idat.vpair += pot_temp; |
| 365 |
> |
*(idat.vpair) += pot_temp; |
| 366 |
|
|
| 367 |
< |
RealType dudr = drhodr * (idat.dfrho1 + idat.dfrho2) + dvpdr; |
| 367 |
> |
RealType dudr = drhodr * ( *(idat.dfrho1) + *(idat.dfrho2) ) + dvpdr; |
| 368 |
|
|
| 369 |
< |
idat.f1 += idat.d * dudr / idat.rij; |
| 369 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij) ; |
| 370 |
|
|
| 371 |
< |
// particle_pot is the difference between the full potential |
| 372 |
< |
// and the full potential without the presence of a particular |
| 371 |
> |
// particlePot is the difference between the full potential and |
| 372 |
> |
// the full potential without the presence of a particular |
| 373 |
|
// particle (atom1). |
| 374 |
|
// |
| 375 |
< |
// This reduces the density at other particle locations, so |
| 376 |
< |
// we need to recompute the density at atom2 assuming atom1 |
| 377 |
< |
// didn't contribute. This then requires recomputing the |
| 378 |
< |
// density functional for atom2 as well. |
| 379 |
< |
// |
| 380 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 381 |
< |
// pair interaction, and will be handled by vpair. |
| 375 |
> |
// This reduces the density at other particle locations, so we |
| 376 |
> |
// need to recompute the density at atom2 assuming atom1 didn't |
| 377 |
> |
// contribute. This then requires recomputing the density |
| 378 |
> |
// functional for atom2 as well. |
| 379 |
> |
|
| 380 |
> |
*(idat.particlePot1) -= data2.c * data2.epsilon * |
| 381 |
> |
sqrt( *(idat.rho2) - rhtmp) + *(idat.frho2); |
| 382 |
> |
|
| 383 |
> |
*(idat.particlePot2) -= data1.c * data1.epsilon * |
| 384 |
> |
sqrt( *(idat.rho1) - rhtmp) + *(idat.frho1); |
| 385 |
|
|
| 386 |
< |
idat.fshift1 = - data1.c * data1.epsilon * sqrt(idat.rho1 - rhtmp); |
| 381 |
< |
idat.fshift2 = - data2.c * data2.epsilon * sqrt(idat.rho2 - rhtmp); |
| 382 |
< |
|
| 383 |
< |
idat.pot += pot_temp; |
| 386 |
> |
(*(idat.pot))[METALLIC_FAMILY] += pot_temp; |
| 387 |
|
} |
| 388 |
|
|
| 389 |
|
return; |
| 390 |
|
} |
| 391 |
|
|
| 392 |
< |
RealType SC::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 392 |
> |
RealType SC::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 393 |
|
if (!initialized_) initialize(); |
| 394 |
< |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 394 |
> |
|
| 395 |
|
map<pair<AtomType*, AtomType*>, SCInteractionData>::iterator it; |
| 396 |
< |
it = MixingMap.find(key); |
| 396 |
> |
it = MixingMap.find(atypes); |
| 397 |
|
if (it == MixingMap.end()) |
| 398 |
|
return 0.0; |
| 399 |
|
else { |
