| 58 |
|
initialized_ = false; |
| 59 |
|
|
| 60 |
|
MixingMap.clear(); |
| 61 |
< |
SCMap.clear(); |
| 62 |
< |
SClist.clear(); |
| 61 |
> |
SCtypes.clear(); |
| 62 |
> |
SCdata.clear(); |
| 63 |
> |
SCtids.clear(); |
| 64 |
|
} |
| 65 |
|
|
| 66 |
|
RealType SC::getM(AtomType* atomType1, AtomType* atomType2) { |
| 103 |
|
return sqrt(epsilon1 * epsilon2); |
| 104 |
|
} |
| 105 |
|
|
| 106 |
< |
void SC::initialize() { |
| 106 |
> |
void SC::initialize() { |
| 107 |
|
// find all of the SC atom Types: |
| 108 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 109 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 110 |
< |
AtomType* at; |
| 108 |
> |
SCtypes.clear(); |
| 109 |
> |
SCtids.clear(); |
| 110 |
> |
SCdata.clear(); |
| 111 |
> |
MixingMap.clear(); |
| 112 |
> |
nSC_ = 0; |
| 113 |
|
|
| 114 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 115 |
< |
at = atomTypes->nextType(i)) { |
| 116 |
< |
SuttonChenAdapter sca = SuttonChenAdapter(at); |
| 117 |
< |
if (sca.isSuttonChen()) |
| 118 |
< |
addType(at); |
| 119 |
< |
} |
| 114 |
> |
SCtids.resize( forceField_->getNAtomType(), -1); |
| 115 |
> |
|
| 116 |
> |
set<AtomType*>::iterator at; |
| 117 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 118 |
> |
if ((*at)->isSC()) nSC_++; |
| 119 |
> |
} |
| 120 |
> |
SCdata.resize(nSC_); |
| 121 |
> |
MixingMap.resize(nSC_); |
| 122 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 123 |
> |
if ((*at)->isSC()) addType((*at)); |
| 124 |
> |
} |
| 125 |
|
initialized_ = true; |
| 126 |
|
} |
| 127 |
|
|
| 138 |
|
scAtomData.alpha = sca.getAlpha(); |
| 139 |
|
scAtomData.epsilon = sca.getEpsilon(); |
| 140 |
|
scAtomData.rCut = 2.0 * scAtomData.alpha; |
| 141 |
< |
|
| 141 |
> |
|
| 142 |
|
// add it to the map: |
| 143 |
+ |
int atid = atomType->getIdent(); |
| 144 |
+ |
int sctid = SCtypes.size(); |
| 145 |
|
|
| 146 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 147 |
< |
ret = SClist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
| 146 |
> |
pair<set<int>::iterator,bool> ret; |
| 147 |
> |
ret = SCtypes.insert( atid ); |
| 148 |
|
if (ret.second == false) { |
| 149 |
|
sprintf( painCave.errMsg, |
| 150 |
|
"SC already had a previous entry with ident %d\n", |
| 151 |
< |
atomType->getIdent() ); |
| 151 |
> |
atid ); |
| 152 |
|
painCave.severity = OPENMD_INFO; |
| 153 |
|
painCave.isFatal = 0; |
| 154 |
|
simError(); |
| 155 |
|
} |
| 146 |
– |
|
| 147 |
– |
SCMap[atomType] = scAtomData; |
| 156 |
|
|
| 157 |
+ |
SCtids[atid] = sctid; |
| 158 |
+ |
SCdata[sctid] = scAtomData; |
| 159 |
+ |
MixingMap[sctid].resize(nSC_); |
| 160 |
+ |
|
| 161 |
|
// Now, iterate over all known types and add to the mixing map: |
| 162 |
|
|
| 163 |
< |
map<AtomType*, SCAtomData>::iterator it; |
| 164 |
< |
for( it = SCMap.begin(); it != SCMap.end(); ++it) { |
| 163 |
> |
std::set<int>::iterator it; |
| 164 |
> |
for( it = SCtypes.begin(); it != SCtypes.end(); ++it) { |
| 165 |
|
|
| 166 |
< |
AtomType* atype2 = (*it).first; |
| 166 |
> |
int sctid2 = SCtids[ (*it) ]; |
| 167 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 168 |
|
|
| 169 |
|
SCInteractionData mixer; |
| 170 |
|
|
| 203 |
|
|
| 204 |
|
mixer.explicitlySet = false; |
| 205 |
|
|
| 206 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 194 |
< |
key1 = make_pair(atomType, atype2); |
| 195 |
< |
key2 = make_pair(atype2, atomType); |
| 206 |
> |
MixingMap[sctid2].resize( nSC_ ); |
| 207 |
|
|
| 208 |
< |
MixingMap[key1] = mixer; |
| 209 |
< |
if (key2 != key1) { |
| 210 |
< |
MixingMap[key2] = mixer; |
| 208 |
> |
MixingMap[sctid][sctid2] = mixer; |
| 209 |
> |
if (sctid2 != sctid) { |
| 210 |
> |
MixingMap[sctid2][sctid] = mixer; |
| 211 |
|
} |
| 212 |
|
} |
| 213 |
|
return; |
| 258 |
|
|
| 259 |
|
mixer.explicitlySet = true; |
| 260 |
|
|
| 261 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 262 |
< |
key1 = make_pair(atype1, atype2); |
| 263 |
< |
key2 = make_pair(atype2, atype1); |
| 264 |
< |
|
| 265 |
< |
MixingMap[key1] = mixer; |
| 266 |
< |
if (key2 != key1) { |
| 256 |
< |
MixingMap[key2] = mixer; |
| 261 |
> |
int sctid1 = SCtids[ atype1->getIdent() ]; |
| 262 |
> |
int sctid2 = SCtids[ atype2->getIdent() ]; |
| 263 |
> |
|
| 264 |
> |
MixingMap[sctid1][sctid2] = mixer; |
| 265 |
> |
if (sctid2 != sctid1) { |
| 266 |
> |
MixingMap[sctid2][sctid1] = mixer; |
| 267 |
|
} |
| 268 |
|
return; |
| 269 |
|
} |
| 271 |
|
void SC::calcDensity(InteractionData &idat) { |
| 272 |
|
|
| 273 |
|
if (!initialized_) initialize(); |
| 274 |
+ |
int sctid1 = SCtids[idat.atid1]; |
| 275 |
+ |
int sctid2 = SCtids[idat.atid2]; |
| 276 |
|
|
| 277 |
< |
SCInteractionData mixer = MixingMap[ idat.atypes ]; |
| 277 |
> |
SCInteractionData &mixer = MixingMap[sctid1][sctid2]; |
| 278 |
|
|
| 279 |
|
RealType rcij = mixer.rCut; |
| 280 |
|
|
| 291 |
|
|
| 292 |
|
if (!initialized_) initialize(); |
| 293 |
|
|
| 294 |
< |
SCAtomData data1 = SCMap[sdat.atype]; |
| 294 |
> |
SCAtomData &data1 = SCdata[SCtids[sdat.atid]]; |
| 295 |
|
|
| 296 |
|
RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) ); |
| 297 |
|
*(sdat.frho) = u; |
| 310 |
|
|
| 311 |
|
if (!initialized_) initialize(); |
| 312 |
|
|
| 313 |
< |
SCAtomData data1 = SCMap[idat.atypes.first]; |
| 314 |
< |
SCAtomData data2 = SCMap[idat.atypes.second]; |
| 313 |
> |
int &sctid1 = SCtids[idat.atid1]; |
| 314 |
> |
int &sctid2 = SCtids[idat.atid2]; |
| 315 |
|
|
| 316 |
< |
SCInteractionData mixer = MixingMap[idat.atypes]; |
| 316 |
> |
SCAtomData &data1 = SCdata[sctid1]; |
| 317 |
> |
SCAtomData &data2 = SCdata[sctid2]; |
| 318 |
|
|
| 319 |
+ |
SCInteractionData &mixer = MixingMap[sctid1][sctid2]; |
| 320 |
+ |
|
| 321 |
|
RealType rcij = mixer.rCut; |
| 322 |
|
|
| 323 |
|
if ( *(idat.rij) < rcij) { |
| 324 |
< |
RealType vcij = mixer.vCut; |
| 324 |
> |
RealType vcij = mixer.vCut; |
| 325 |
> |
RealType rhtmp, drhodr, vptmp, dvpdr; |
| 326 |
|
|
| 327 |
< |
pair<RealType, RealType> res; |
| 327 |
> |
mixer.phi->getValueAndDerivativeAt( *(idat.rij), rhtmp, drhodr ); |
| 328 |
> |
mixer.V->getValueAndDerivativeAt( *(idat.rij), vptmp, dvpdr); |
| 329 |
|
|
| 313 |
– |
res = mixer.phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 314 |
– |
RealType rhtmp = res.first; |
| 315 |
– |
RealType drhodr = res.second; |
| 316 |
– |
|
| 317 |
– |
res = mixer.V->getValueAndDerivativeAt( *(idat.rij) ); |
| 318 |
– |
RealType vptmp = res.first; |
| 319 |
– |
RealType dvpdr = res.second; |
| 320 |
– |
|
| 330 |
|
RealType pot_temp = vptmp - vcij; |
| 331 |
|
*(idat.vpair) += pot_temp; |
| 332 |
|
|
| 360 |
|
RealType SC::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 361 |
|
if (!initialized_) initialize(); |
| 362 |
|
|
| 363 |
< |
map<pair<AtomType*, AtomType*>, SCInteractionData>::iterator it; |
| 364 |
< |
it = MixingMap.find(atypes); |
| 365 |
< |
if (it == MixingMap.end()) |
| 363 |
> |
int atid1 = atypes.first->getIdent(); |
| 364 |
> |
int atid2 = atypes.second->getIdent(); |
| 365 |
> |
int &sctid1 = SCtids[atid1]; |
| 366 |
> |
int &sctid2 = SCtids[atid2]; |
| 367 |
> |
|
| 368 |
> |
if (sctid1 == -1 || sctid2 == -1) { |
| 369 |
|
return 0.0; |
| 370 |
< |
else { |
| 371 |
< |
SCInteractionData mixer = (*it).second; |
| 360 |
< |
return mixer.rCut; |
| 370 |
> |
} else { |
| 371 |
> |
return MixingMap[sctid1][sctid2].rCut; |
| 372 |
|
} |
| 373 |
|
} |
| 374 |
|
} |
