| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 60 |
|
CubicSpline* z1 = ea1.getZ(); |
| 61 |
|
CubicSpline* z2 = ea2.getZ(); |
| 62 |
|
|
| 63 |
+ |
// Thise prefactors convert the charge-charge interactions into |
| 64 |
+ |
// kcal / mol all were computed assuming distances are measured in |
| 65 |
+ |
// angstroms Charge-Charge, assuming charges are measured in |
| 66 |
+ |
// electrons. Matches value in Electrostatics.cpp |
| 67 |
+ |
pre11_ = 332.0637778; |
| 68 |
+ |
|
| 69 |
|
// make the r grid: |
| 70 |
|
|
| 65 |
– |
|
| 71 |
|
// we need phi out to the largest value we'll encounter in the radial space; |
| 72 |
|
|
| 73 |
|
RealType rmax = 0.0; |
| 106 |
|
zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0; |
| 107 |
|
zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0; |
| 108 |
|
|
| 109 |
< |
phi = 331.999296 * (zi * zj) / r; |
| 110 |
< |
|
| 109 |
> |
phi = pre11_ * (zi * zj) / r; |
| 110 |
> |
|
| 111 |
|
phivals.push_back(phi); |
| 112 |
|
} |
| 108 |
– |
|
| 113 |
|
CubicSpline* cs = new CubicSpline(); |
| 114 |
|
cs->addPoints(rvals, phivals); |
| 115 |
|
return cs; |
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
void EAM::initialize() { |
| 120 |
– |
|
| 124 |
|
// set up the mixing method: |
| 125 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 126 |
|
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 134 |
|
mixMeth_ = eamUnknown; |
| 135 |
|
|
| 136 |
|
// find all of the EAM atom Types: |
| 137 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 138 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 139 |
< |
AtomType* at; |
| 137 |
> |
EAMtypes.clear(); |
| 138 |
> |
EAMtids.clear(); |
| 139 |
> |
EAMdata.clear(); |
| 140 |
> |
MixingMap.clear(); |
| 141 |
> |
nEAM_ = 0; |
| 142 |
> |
|
| 143 |
> |
EAMtids.resize( forceField_->getNAtomType(), -1); |
| 144 |
|
|
| 145 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 146 |
< |
at = atomTypes->nextType(i)) { |
| 147 |
< |
|
| 141 |
< |
if (at->isEAM()) |
| 142 |
< |
addType(at); |
| 145 |
> |
set<AtomType*>::iterator at; |
| 146 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 147 |
> |
if ((*at)->isEAM()) nEAM_++; |
| 148 |
|
} |
| 149 |
+ |
EAMdata.resize(nEAM_); |
| 150 |
+ |
MixingMap.resize(nEAM_); |
| 151 |
+ |
|
| 152 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 153 |
+ |
if ((*at)->isEAM()) addType(*at); |
| 154 |
+ |
} |
| 155 |
|
|
| 156 |
|
// find all of the explicit EAM interactions (setfl): |
| 157 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 211 |
|
eamAtomData.F = ea.getF(); |
| 212 |
|
eamAtomData.Z = ea.getZ(); |
| 213 |
|
eamAtomData.rcut = ea.getRcut(); |
| 214 |
< |
|
| 214 |
> |
|
| 215 |
|
// add it to the map: |
| 216 |
+ |
int atid = atomType->getIdent(); |
| 217 |
+ |
int eamtid = EAMtypes.size(); |
| 218 |
|
|
| 219 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 220 |
< |
ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
| 219 |
> |
pair<set<int>::iterator,bool> ret; |
| 220 |
> |
ret = EAMtypes.insert( atid ); |
| 221 |
|
if (ret.second == false) { |
| 222 |
|
sprintf( painCave.errMsg, |
| 223 |
|
"EAM already had a previous entry with ident %d\n", |
| 224 |
< |
atomType->getIdent()); |
| 224 |
> |
atid); |
| 225 |
|
painCave.severity = OPENMD_INFO; |
| 226 |
|
painCave.isFatal = 0; |
| 227 |
|
simError(); |
| 228 |
|
} |
| 229 |
|
|
| 230 |
< |
EAMMap[atomType] = eamAtomData; |
| 230 |
> |
|
| 231 |
> |
EAMtids[atid] = eamtid; |
| 232 |
> |
EAMdata[eamtid] = eamAtomData; |
| 233 |
> |
MixingMap[eamtid].resize(nEAM_); |
| 234 |
|
|
| 235 |
|
// Now, iterate over all known types and add to the mixing map: |
| 236 |
|
|
| 237 |
< |
map<AtomType*, EAMAtomData>::iterator it; |
| 238 |
< |
for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
| 237 |
> |
std::set<int>::iterator it; |
| 238 |
> |
for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) { |
| 239 |
|
|
| 240 |
< |
AtomType* atype2 = (*it).first; |
| 240 |
> |
int eamtid2 = EAMtids[ (*it) ]; |
| 241 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 242 |
|
|
| 243 |
|
EAMInteractionData mixer; |
| 244 |
|
mixer.phi = getPhi(atomType, atype2); |
| 245 |
+ |
mixer.rcut = mixer.phi->getLimits().second; |
| 246 |
|
mixer.explicitlySet = false; |
| 247 |
|
|
| 248 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 231 |
< |
key1 = make_pair(atomType, atype2); |
| 232 |
< |
key2 = make_pair(atype2, atomType); |
| 248 |
> |
MixingMap[eamtid2].resize( nEAM_ ); |
| 249 |
|
|
| 250 |
< |
MixingMap[key1] = mixer; |
| 251 |
< |
if (key2 != key1) { |
| 252 |
< |
MixingMap[key2] = mixer; |
| 250 |
> |
MixingMap[eamtid][eamtid2] = mixer; |
| 251 |
> |
if (eamtid2 != eamtid) { |
| 252 |
> |
MixingMap[eamtid2][eamtid] = mixer; |
| 253 |
|
} |
| 254 |
|
} |
| 255 |
|
return; |
| 271 |
|
|
| 272 |
|
cs->addPoints(rVals, phiVals); |
| 273 |
|
mixer.phi = cs; |
| 274 |
+ |
mixer.rcut = mixer.phi->getLimits().second; |
| 275 |
|
mixer.explicitlySet = true; |
| 276 |
|
|
| 277 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 278 |
< |
key1 = make_pair(atype1, atype2); |
| 262 |
< |
key2 = make_pair(atype2, atype1); |
| 277 |
> |
int eamtid1 = EAMtids[ atype1->getIdent() ]; |
| 278 |
> |
int eamtid2 = EAMtids[ atype2->getIdent() ]; |
| 279 |
|
|
| 280 |
< |
MixingMap[key1] = mixer; |
| 281 |
< |
if (key2 != key1) { |
| 282 |
< |
MixingMap[key2] = mixer; |
| 280 |
> |
MixingMap[eamtid1][eamtid2] = mixer; |
| 281 |
> |
if (eamtid2 != eamtid1) { |
| 282 |
> |
MixingMap[eamtid2][eamtid1] = mixer; |
| 283 |
|
} |
| 284 |
|
return; |
| 285 |
|
} |
| 288 |
|
|
| 289 |
|
if (!initialized_) initialize(); |
| 290 |
|
|
| 291 |
< |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 292 |
< |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 293 |
< |
|
| 291 |
> |
EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]]; |
| 292 |
> |
EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]]; |
| 293 |
> |
|
| 294 |
|
if (haveCutoffRadius_) |
| 295 |
|
if ( *(idat.rij) > eamRcut_) return; |
| 296 |
|
|
| 297 |
< |
if ( *(idat.rij) < data1.rcut) |
| 298 |
< |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 299 |
< |
|
| 297 |
> |
if ( *(idat.rij) < data1.rcut) { |
| 298 |
> |
*(idat.rho2) += data1.rho->getValueAt( *(idat.rij)); |
| 299 |
> |
} |
| 300 |
|
|
| 301 |
< |
if ( *(idat.rij) < data2.rcut) |
| 302 |
< |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 301 |
> |
if ( *(idat.rij) < data2.rcut) { |
| 302 |
> |
*(idat.rho1) += data2.rho->getValueAt( *(idat.rij)); |
| 303 |
> |
} |
| 304 |
|
|
| 305 |
|
return; |
| 306 |
|
} |
| 308 |
|
void EAM::calcFunctional(SelfData &sdat) { |
| 309 |
|
|
| 310 |
|
if (!initialized_) initialize(); |
| 311 |
+ |
EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ]; |
| 312 |
+ |
|
| 313 |
+ |
data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), |
| 314 |
+ |
*(sdat.dfrhodrho) ); |
| 315 |
|
|
| 316 |
< |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 296 |
< |
|
| 297 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 298 |
< |
|
| 299 |
< |
*(sdat.frho) = result.first; |
| 300 |
< |
*(sdat.dfrhodrho) = result.second; |
| 301 |
< |
|
| 302 |
< |
(*(sdat.pot))[METALLIC_FAMILY] += result.first; |
| 316 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho); |
| 317 |
|
if (sdat.doParticlePot) { |
| 318 |
< |
*(sdat.particlePot) += result.first; |
| 318 |
> |
*(sdat.particlePot) += *(sdat.frho); |
| 319 |
|
} |
| 320 |
|
|
| 321 |
|
return; |
| 329 |
|
if (haveCutoffRadius_) |
| 330 |
|
if ( *(idat.rij) > eamRcut_) return; |
| 331 |
|
|
| 332 |
< |
pair<RealType, RealType> res; |
| 332 |
> |
|
| 333 |
> |
int eamtid1 = EAMtids[idat.atid1]; |
| 334 |
> |
int eamtid2 = EAMtids[idat.atid2]; |
| 335 |
> |
EAMAtomData &data1 = EAMdata[eamtid1]; |
| 336 |
> |
EAMAtomData &data2 = EAMdata[eamtid2]; |
| 337 |
|
|
| 320 |
– |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 321 |
– |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 322 |
– |
|
| 338 |
|
// get type-specific cutoff radii |
| 339 |
|
|
| 340 |
|
RealType rci = data1.rcut; |
| 341 |
|
RealType rcj = data2.rcut; |
| 342 |
+ |
|
| 343 |
|
|
| 344 |
|
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 345 |
|
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 347 |
|
RealType drhoidr, drhojdr, dudr; |
| 348 |
|
|
| 349 |
|
if ( *(idat.rij) < rci) { |
| 350 |
< |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 351 |
< |
rha = res.first; |
| 352 |
< |
drha = res.second; |
| 337 |
< |
|
| 338 |
< |
res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 339 |
< |
pha = res.first; |
| 340 |
< |
dpha = res.second; |
| 350 |
> |
data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha); |
| 351 |
> |
CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi; |
| 352 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha); |
| 353 |
|
} |
| 354 |
|
|
| 355 |
|
if ( *(idat.rij) < rcj) { |
| 356 |
< |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 357 |
< |
rhb = res.first; |
| 358 |
< |
drhb = res.second; |
| 347 |
< |
|
| 348 |
< |
res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 349 |
< |
phb = res.first; |
| 350 |
< |
dphb = res.second; |
| 356 |
> |
data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb ); |
| 357 |
> |
CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi; |
| 358 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb); |
| 359 |
|
} |
| 352 |
– |
|
| 360 |
|
switch(mixMeth_) { |
| 361 |
|
case eamJohnson: |
| 355 |
– |
|
| 362 |
|
if ( *(idat.rij) < rci) { |
| 363 |
|
phab = phab + 0.5 * (rhb / rha) * pha; |
| 364 |
|
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 365 |
|
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 366 |
|
} |
| 367 |
< |
|
| 362 |
< |
|
| 363 |
< |
|
| 367 |
> |
|
| 368 |
|
if ( *(idat.rij) < rcj) { |
| 369 |
|
phab = phab + 0.5 * (rha / rhb) * phb; |
| 370 |
|
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 371 |
|
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 372 |
|
} |
| 369 |
– |
|
| 373 |
|
break; |
| 371 |
– |
|
| 374 |
|
case eamDaw: |
| 375 |
< |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 376 |
< |
phab = res.first; |
| 377 |
< |
dvpdr = res.second; |
| 378 |
< |
|
| 375 |
> |
if ( *(idat.rij) < MixingMap[eamtid1][eamtid2].rcut) { |
| 376 |
> |
MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), |
| 377 |
> |
phab, dvpdr); |
| 378 |
> |
} |
| 379 |
|
break; |
| 380 |
|
case eamUnknown: |
| 381 |
|
default: |
| 395 |
|
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 396 |
|
|
| 397 |
|
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 398 |
< |
|
| 398 |
> |
|
| 399 |
|
if (idat.doParticlePot) { |
| 400 |
|
// particlePot is the difference between the full potential and |
| 401 |
|
// the full potential without the presence of a particular |
| 413 |
|
- *(idat.frho1); |
| 414 |
|
} |
| 415 |
|
|
| 416 |
< |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 417 |
< |
|
| 418 |
< |
*(idat.vpair) += phab; |
| 417 |
< |
|
| 418 |
< |
return; |
| 419 |
< |
|
| 416 |
> |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 417 |
> |
*(idat.vpair) += phab; |
| 418 |
> |
return; |
| 419 |
|
} |
| 420 |
|
|
| 421 |
|
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 423 |
|
|
| 424 |
|
RealType cut = 0.0; |
| 425 |
|
|
| 426 |
< |
map<AtomType*, EAMAtomData>::iterator it; |
| 427 |
< |
|
| 428 |
< |
it = EAMMap.find(atypes.first); |
| 429 |
< |
if (it != EAMMap.end()) { |
| 430 |
< |
EAMAtomData data1 = (*it).second; |
| 426 |
> |
int atid1 = atypes.first->getIdent(); |
| 427 |
> |
int atid2 = atypes.second->getIdent(); |
| 428 |
> |
int eamtid1 = EAMtids[atid1]; |
| 429 |
> |
int eamtid2 = EAMtids[atid2]; |
| 430 |
> |
|
| 431 |
> |
if (eamtid1 != -1) { |
| 432 |
> |
EAMAtomData data1 = EAMdata[eamtid1]; |
| 433 |
|
cut = data1.rcut; |
| 434 |
|
} |
| 435 |
|
|
| 436 |
< |
it = EAMMap.find(atypes.second); |
| 437 |
< |
if (it != EAMMap.end()) { |
| 437 |
< |
EAMAtomData data2 = (*it).second; |
| 436 |
> |
if (eamtid2 != -1) { |
| 437 |
> |
EAMAtomData data2 = EAMdata[eamtid2]; |
| 438 |
|
if (data2.rcut > cut) |
| 439 |
|
cut = data2.rcut; |
| 440 |
|
} |
| 441 |
< |
|
| 441 |
> |
|
| 442 |
|
return cut; |
| 443 |
|
} |
| 444 |
|
} |
