| 117 |
|
} |
| 118 |
|
|
| 119 |
|
void EAM::initialize() { |
| 120 |
– |
|
| 120 |
|
// set up the mixing method: |
| 121 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 122 |
|
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 130 |
|
mixMeth_ = eamUnknown; |
| 131 |
|
|
| 132 |
|
// find all of the EAM atom Types: |
| 133 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 134 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 135 |
< |
AtomType* at; |
| 133 |
> |
EAMtypes.clear(); |
| 134 |
> |
EAMtids.clear(); |
| 135 |
> |
EAMdata.clear(); |
| 136 |
> |
MixingMap.clear(); |
| 137 |
> |
nEAM_ = 0; |
| 138 |
> |
|
| 139 |
> |
EAMtids.resize( forceField_->getNAtomType(), -1); |
| 140 |
|
|
| 141 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 142 |
< |
at = atomTypes->nextType(i)) { |
| 143 |
< |
|
| 141 |
< |
if (at->isEAM()) |
| 142 |
< |
addType(at); |
| 141 |
> |
set<AtomType*>::iterator at; |
| 142 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 143 |
> |
if ((*at)->isEAM()) nEAM_++; |
| 144 |
|
} |
| 145 |
+ |
EAMdata.resize(nEAM_); |
| 146 |
+ |
MixingMap.resize(nEAM_); |
| 147 |
+ |
|
| 148 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 149 |
+ |
if ((*at)->isEAM()) addType(*at); |
| 150 |
+ |
} |
| 151 |
|
|
| 152 |
|
// find all of the explicit EAM interactions (setfl): |
| 153 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 209 |
|
eamAtomData.rcut = ea.getRcut(); |
| 210 |
|
|
| 211 |
|
// add it to the map: |
| 212 |
+ |
int atid = atomType->getIdent(); |
| 213 |
+ |
int eamtid = EAMtypes.size(); |
| 214 |
|
|
| 215 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 216 |
< |
ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
| 215 |
> |
pair<set<int>::iterator,bool> ret; |
| 216 |
> |
ret = EAMtypes.insert( atid ); |
| 217 |
|
if (ret.second == false) { |
| 218 |
|
sprintf( painCave.errMsg, |
| 219 |
|
"EAM already had a previous entry with ident %d\n", |
| 220 |
< |
atomType->getIdent()); |
| 220 |
> |
atid); |
| 221 |
|
painCave.severity = OPENMD_INFO; |
| 222 |
|
painCave.isFatal = 0; |
| 223 |
|
simError(); |
| 224 |
|
} |
| 225 |
|
|
| 226 |
< |
EAMMap[atomType] = eamAtomData; |
| 226 |
> |
EAMtids[atid] = eamtid; |
| 227 |
> |
EAMdata[eamtid] = eamAtomData; |
| 228 |
> |
MixingMap[eamtid].resize(nEAM_); |
| 229 |
|
|
| 230 |
|
// Now, iterate over all known types and add to the mixing map: |
| 231 |
|
|
| 232 |
< |
map<AtomType*, EAMAtomData>::iterator it; |
| 233 |
< |
for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
| 232 |
> |
std::set<int>::iterator it; |
| 233 |
> |
for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) { |
| 234 |
|
|
| 235 |
< |
AtomType* atype2 = (*it).first; |
| 235 |
> |
int eamtid2 = EAMtids[ (*it) ]; |
| 236 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 237 |
|
|
| 238 |
|
EAMInteractionData mixer; |
| 239 |
|
mixer.phi = getPhi(atomType, atype2); |
| 240 |
|
mixer.explicitlySet = false; |
| 241 |
|
|
| 242 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 231 |
< |
key1 = make_pair(atomType, atype2); |
| 232 |
< |
key2 = make_pair(atype2, atomType); |
| 242 |
> |
MixingMap[eamtid2].resize( nEAM_ ); |
| 243 |
|
|
| 244 |
< |
MixingMap[key1] = mixer; |
| 245 |
< |
if (key2 != key1) { |
| 246 |
< |
MixingMap[key2] = mixer; |
| 244 |
> |
MixingMap[eamtid][eamtid2] = mixer; |
| 245 |
> |
if (eamtid2 != eamtid) { |
| 246 |
> |
MixingMap[eamtid2][eamtid] = mixer; |
| 247 |
|
} |
| 248 |
|
} |
| 249 |
|
return; |
| 267 |
|
mixer.phi = cs; |
| 268 |
|
mixer.explicitlySet = true; |
| 269 |
|
|
| 270 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 271 |
< |
key1 = make_pair(atype1, atype2); |
| 262 |
< |
key2 = make_pair(atype2, atype1); |
| 270 |
> |
int eamtid1 = EAMtids[ atype1->getIdent() ]; |
| 271 |
> |
int eamtid2 = EAMtids[ atype2->getIdent() ]; |
| 272 |
|
|
| 273 |
< |
MixingMap[key1] = mixer; |
| 274 |
< |
if (key2 != key1) { |
| 275 |
< |
MixingMap[key2] = mixer; |
| 273 |
> |
MixingMap[eamtid1][eamtid2] = mixer; |
| 274 |
> |
if (eamtid2 != eamtid1) { |
| 275 |
> |
MixingMap[eamtid2][eamtid1] = mixer; |
| 276 |
|
} |
| 277 |
|
return; |
| 278 |
|
} |
| 281 |
|
|
| 282 |
|
if (!initialized_) initialize(); |
| 283 |
|
|
| 284 |
< |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 285 |
< |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 286 |
< |
|
| 284 |
> |
EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]]; |
| 285 |
> |
EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]]; |
| 286 |
> |
|
| 287 |
|
if (haveCutoffRadius_) |
| 288 |
|
if ( *(idat.rij) > eamRcut_) return; |
| 289 |
|
|
| 301 |
|
|
| 302 |
|
if (!initialized_) initialize(); |
| 303 |
|
|
| 304 |
< |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 304 |
> |
EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ]; |
| 305 |
|
|
| 306 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 306 |
> |
data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), *(sdat.dfrhodrho) ); |
| 307 |
|
|
| 308 |
< |
*(sdat.frho) = result.first; |
| 300 |
< |
*(sdat.dfrhodrho) = result.second; |
| 301 |
< |
|
| 302 |
< |
(*(sdat.pot))[METALLIC_FAMILY] += result.first; |
| 308 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho); |
| 309 |
|
if (sdat.doParticlePot) { |
| 310 |
< |
*(sdat.particlePot) += result.first; |
| 310 |
> |
*(sdat.particlePot) += *(sdat.frho); |
| 311 |
|
} |
| 312 |
|
|
| 313 |
|
return; |
| 321 |
|
if (haveCutoffRadius_) |
| 322 |
|
if ( *(idat.rij) > eamRcut_) return; |
| 323 |
|
|
| 324 |
< |
pair<RealType, RealType> res; |
| 324 |
> |
|
| 325 |
> |
int eamtid1 = EAMtids[idat.atid1]; |
| 326 |
> |
int eamtid2 = EAMtids[idat.atid2]; |
| 327 |
|
|
| 328 |
< |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 329 |
< |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 328 |
> |
EAMAtomData &data1 = EAMdata[eamtid1]; |
| 329 |
> |
EAMAtomData &data2 = EAMdata[eamtid2]; |
| 330 |
|
|
| 331 |
|
// get type-specific cutoff radii |
| 332 |
|
|
| 339 |
|
RealType drhoidr, drhojdr, dudr; |
| 340 |
|
|
| 341 |
|
if ( *(idat.rij) < rci) { |
| 342 |
< |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 343 |
< |
rha = res.first; |
| 344 |
< |
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; |
| 342 |
> |
data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha); |
| 343 |
> |
CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi; |
| 344 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha); |
| 345 |
|
} |
| 346 |
|
|
| 347 |
|
if ( *(idat.rij) < rcj) { |
| 348 |
< |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 349 |
< |
rhb = res.first; |
| 350 |
< |
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; |
| 348 |
> |
data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb ); |
| 349 |
> |
CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi; |
| 350 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb); |
| 351 |
|
} |
| 352 |
|
|
| 353 |
|
switch(mixMeth_) { |
| 370 |
|
break; |
| 371 |
|
|
| 372 |
|
case eamDaw: |
| 373 |
< |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 374 |
< |
phab = res.first; |
| 375 |
< |
dvpdr = res.second; |
| 373 |
> |
MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr); |
| 374 |
|
|
| 375 |
|
break; |
| 376 |
|
case eamUnknown: |
| 422 |
|
|
| 423 |
|
RealType cut = 0.0; |
| 424 |
|
|
| 425 |
< |
map<AtomType*, EAMAtomData>::iterator it; |
| 426 |
< |
|
| 427 |
< |
it = EAMMap.find(atypes.first); |
| 428 |
< |
if (it != EAMMap.end()) { |
| 429 |
< |
EAMAtomData data1 = (*it).second; |
| 425 |
> |
int atid1 = atypes.first->getIdent(); |
| 426 |
> |
int atid2 = atypes.second->getIdent(); |
| 427 |
> |
int eamtid1 = EAMtids[atid1]; |
| 428 |
> |
int eamtid2 = EAMtids[atid2]; |
| 429 |
> |
|
| 430 |
> |
if (eamtid1 != -1) { |
| 431 |
> |
EAMAtomData data1 = EAMdata[eamtid1]; |
| 432 |
|
cut = data1.rcut; |
| 433 |
|
} |
| 434 |
|
|
| 435 |
< |
it = EAMMap.find(atypes.second); |
| 436 |
< |
if (it != EAMMap.end()) { |
| 437 |
< |
EAMAtomData data2 = (*it).second; |
| 435 |
> |
if (eamtid2 != -1) { |
| 436 |
> |
EAMAtomData data2 = EAMdata[eamtid2]; |
| 437 |
|
if (data2.rcut > cut) |
| 438 |
|
cut = data2.rcut; |
| 439 |
|
} |
| 440 |
< |
|
| 440 |
> |
|
| 441 |
|
return cut; |
| 442 |
|
} |
| 443 |
|
} |
