| 54 |
|
RealType EAM::eamRcut_ = 0.0; |
| 55 |
|
EAMMixingMethod EAM::mixMeth_ = eamJohnson; |
| 56 |
|
ForceField* EAM::forceField_ = NULL; |
| 57 |
< |
std::map<int, AtomType*> EAM::EAMlist; |
| 58 |
< |
std::map<AtomType*, EAMAtomData> EAM::EAMMap; |
| 59 |
< |
std::map<std::pair<AtomType*, AtomType*>, EAMInteractionData> EAM::MixingMap; |
| 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; |
| 161 |
|
|
| 162 |
|
// make the r grid: |
| 163 |
|
|
| 164 |
– |
// set rcut to be the smaller of the two atomic rcuts |
| 164 |
|
|
| 165 |
< |
RealType rcut = eamParam1.rcut < eamParam2.rcut ? |
| 166 |
< |
eamParam1.rcut : eamParam2.rcut; |
| 165 |
> |
// we need phi out to the largest value we'll encounter in the radial space; |
| 166 |
> |
|
| 167 |
> |
RealType rmax = 0.0; |
| 168 |
> |
rmax = max(rmax, eamParam1.rcut); |
| 169 |
> |
rmax = max(rmax, eamParam1.nr * eamParam1.dr); |
| 170 |
|
|
| 171 |
+ |
rmax = max(rmax, eamParam2.rcut); |
| 172 |
+ |
rmax = max(rmax, eamParam2.nr * eamParam2.dr); |
| 173 |
+ |
|
| 174 |
|
// use the smallest dr (finest grid) to build our grid: |
| 175 |
|
|
| 176 |
< |
RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr; |
| 177 |
< |
int nr = int(rcut/dr); |
| 176 |
> |
RealType dr = min(eamParam1.dr, eamParam2.dr); |
| 177 |
> |
|
| 178 |
> |
int nr = int(rmax/dr + 0.5); |
| 179 |
> |
|
| 180 |
|
vector<RealType> rvals; |
| 181 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i*dr); |
| 181 |
> |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); |
| 182 |
|
|
| 183 |
|
// construct the pair potential: |
| 184 |
|
|
| 191 |
|
|
| 192 |
|
for (int i = 1; i < rvals.size(); i++ ) { |
| 193 |
|
r = rvals[i]; |
| 194 |
< |
zi = z1->getValueAt(r); |
| 195 |
< |
zj = z2->getValueAt(r); |
| 194 |
> |
|
| 195 |
> |
// only use z(r) if we're inside this atoms cutoff radius, otherwise, we'll use zero for the charge. |
| 196 |
> |
// This effectively means that our phi grid goes out beyond the cutoff of the pair potential |
| 197 |
> |
|
| 198 |
> |
zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; |
| 199 |
> |
zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; |
| 200 |
|
|
| 201 |
|
phi = 331.999296 * (zi * zj) / r; |
| 202 |
+ |
|
| 203 |
|
phivals.push_back(phi); |
| 204 |
|
} |
| 205 |
|
|
| 212 |
|
|
| 213 |
|
// set up the mixing method: |
| 214 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 215 |
< |
string EAMMixMeth = toUpperCopy(fopts.getEAMMixingMethod()); |
| 216 |
< |
|
| 215 |
> |
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 216 |
> |
toUpper(EAMMixMeth); |
| 217 |
> |
|
| 218 |
|
if (EAMMixMeth == "JOHNSON") |
| 219 |
|
mixMeth_ = eamJohnson; |
| 220 |
|
else if (EAMMixMeth == "DAW") |
| 244 |
|
|
| 245 |
|
if (nbt->isEAM()) { |
| 246 |
|
|
| 247 |
< |
std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 247 |
> |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 248 |
|
|
| 249 |
|
GenericData* data = nbt->getPropertyByName("EAM"); |
| 250 |
|
if (data == NULL) { |
| 295 |
|
// add it to the map: |
| 296 |
|
AtomTypeProperties atp = atomType->getATP(); |
| 297 |
|
|
| 298 |
< |
std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
| 299 |
< |
ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
| 298 |
> |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 299 |
> |
ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 300 |
|
if (ret.second == false) { |
| 301 |
|
sprintf( painCave.errMsg, |
| 302 |
|
"EAM already had a previous entry with ident %d\n", |
| 310 |
|
|
| 311 |
|
// Now, iterate over all known types and add to the mixing map: |
| 312 |
|
|
| 313 |
< |
std::map<AtomType*, EAMAtomData>::iterator it; |
| 313 |
> |
map<AtomType*, EAMAtomData>::iterator it; |
| 314 |
|
for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
| 315 |
|
|
| 316 |
|
AtomType* atype2 = (*it).first; |
| 319 |
|
mixer.phi = getPhi(atomType, atype2); |
| 320 |
|
mixer.explicitlySet = false; |
| 321 |
|
|
| 322 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 323 |
< |
key1 = std::make_pair(atomType, atype2); |
| 324 |
< |
key2 = std::make_pair(atype2, atomType); |
| 322 |
> |
pair<AtomType*, AtomType*> key1, key2; |
| 323 |
> |
key1 = make_pair(atomType, atype2); |
| 324 |
> |
key2 = make_pair(atype2, atomType); |
| 325 |
|
|
| 326 |
|
MixingMap[key1] = mixer; |
| 327 |
|
if (key2 != key1) { |
| 349 |
|
mixer.phi = cs; |
| 350 |
|
mixer.explicitlySet = true; |
| 351 |
|
|
| 352 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 353 |
< |
key1 = std::make_pair(atype1, atype2); |
| 354 |
< |
key2 = std::make_pair(atype2, atype1); |
| 352 |
> |
pair<AtomType*, AtomType*> key1, key2; |
| 353 |
> |
key1 = make_pair(atype1, atype2); |
| 354 |
> |
key2 = make_pair(atype2, atype1); |
| 355 |
|
|
| 356 |
|
MixingMap[key1] = mixer; |
| 357 |
|
if (key2 != key1) { |
| 396 |
|
RealType &fshift_i, RealType &fshift_j) { |
| 397 |
|
|
| 398 |
|
if (!initialized_) initialize(); |
| 399 |
< |
|
| 399 |
> |
|
| 400 |
|
pair<RealType, RealType> res; |
| 401 |
|
|
| 402 |
|
if (rij < eamRcut_) { |
| 455 |
|
break; |
| 456 |
|
|
| 457 |
|
case eamDaw: |
| 445 |
– |
|
| 458 |
|
res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij); |
| 459 |
|
phab = res.first; |
| 460 |
|
dvpdr = res.second; |
