| 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). |
| 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). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <stdio.h> |
| 51 |
|
|
| 52 |
|
namespace OpenMD { |
| 53 |
|
|
| 54 |
< |
bool EAM::initialized_ = false; |
| 55 |
< |
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; |
| 60 |
< |
|
| 54 |
> |
EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), |
| 55 |
> |
mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {} |
| 56 |
|
|
| 62 |
– |
EAM* EAM::_instance = NULL; |
| 63 |
– |
|
| 64 |
– |
EAM* EAM::Instance() { |
| 65 |
– |
if (!_instance) { |
| 66 |
– |
_instance = new EAM(); |
| 67 |
– |
} |
| 68 |
– |
return _instance; |
| 69 |
– |
} |
| 70 |
– |
|
| 57 |
|
EAMParam EAM::getEAMParam(AtomType* atomType) { |
| 58 |
|
|
| 59 |
|
// Do sanity checking on the AtomType we were passed before |
| 97 |
|
RealType dr = eamParam.dr; |
| 98 |
|
vector<RealType> rvals; |
| 99 |
|
|
| 100 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i * dr); |
| 100 |
> |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
| 101 |
|
|
| 102 |
|
CubicSpline* cs = new CubicSpline(); |
| 103 |
|
cs->addPoints(rvals, eamParam.Z); |
| 115 |
|
RealType dr = eamParam.dr; |
| 116 |
|
vector<RealType> rvals; |
| 117 |
|
|
| 118 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i * dr); |
| 118 |
> |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
| 119 |
|
|
| 120 |
|
CubicSpline* cs = new CubicSpline(); |
| 121 |
|
cs->addPoints(rvals, eamParam.rho); |
| 130 |
|
vector<RealType> scaledF; |
| 131 |
|
|
| 132 |
|
for (int i = 0; i < nrho; i++) { |
| 133 |
< |
rhovals.push_back(i * drho); |
| 133 |
> |
rhovals.push_back(RealType(i) * drho); |
| 134 |
|
scaledF.push_back( eamParam.F[i] * 23.06054 ); |
| 135 |
|
} |
| 136 |
|
|
| 137 |
|
CubicSpline* cs = new CubicSpline(); |
| 138 |
< |
cs->addPoints(rhovals, eamParam.F); |
| 138 |
> |
cs->addPoints(rhovals, scaledF); |
| 139 |
|
return cs; |
| 140 |
|
} |
| 141 |
|
|
| 147 |
|
|
| 148 |
|
// make the r grid: |
| 149 |
|
|
| 164 |
– |
// set rcut to be the smaller of the two atomic rcuts |
| 150 |
|
|
| 151 |
< |
RealType rcut = eamParam1.rcut < eamParam2.rcut ? |
| 152 |
< |
eamParam1.rcut : eamParam2.rcut; |
| 151 |
> |
// we need phi out to the largest value we'll encounter in the radial space; |
| 152 |
> |
|
| 153 |
> |
RealType rmax = 0.0; |
| 154 |
> |
rmax = max(rmax, eamParam1.rcut); |
| 155 |
> |
rmax = max(rmax, eamParam1.nr * eamParam1.dr); |
| 156 |
|
|
| 157 |
+ |
rmax = max(rmax, eamParam2.rcut); |
| 158 |
+ |
rmax = max(rmax, eamParam2.nr * eamParam2.dr); |
| 159 |
+ |
|
| 160 |
|
// use the smallest dr (finest grid) to build our grid: |
| 161 |
|
|
| 162 |
< |
RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr; |
| 163 |
< |
int nr = int(rcut/dr); |
| 162 |
> |
RealType dr = min(eamParam1.dr, eamParam2.dr); |
| 163 |
> |
|
| 164 |
> |
int nr = int(rmax/dr + 0.5); |
| 165 |
> |
|
| 166 |
|
vector<RealType> rvals; |
| 167 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i*dr); |
| 167 |
> |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); |
| 168 |
|
|
| 169 |
|
// construct the pair potential: |
| 170 |
|
|
| 177 |
|
|
| 178 |
|
for (int i = 1; i < rvals.size(); i++ ) { |
| 179 |
|
r = rvals[i]; |
| 180 |
< |
zi = z1->getValueAt(r); |
| 181 |
< |
zj = z2->getValueAt(r); |
| 180 |
> |
|
| 181 |
> |
// only use z(r) if we're inside this atom's cutoff radius, |
| 182 |
> |
// otherwise, we'll use zero for the charge. This effectively |
| 183 |
> |
// means that our phi grid goes out beyond the cutoff of the |
| 184 |
> |
// pair potential |
| 185 |
> |
|
| 186 |
> |
zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; |
| 187 |
> |
zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; |
| 188 |
|
|
| 189 |
|
phi = 331.999296 * (zi * zj) / r; |
| 190 |
+ |
|
| 191 |
|
phivals.push_back(phi); |
| 192 |
|
} |
| 193 |
|
|
| 196 |
|
return cs; |
| 197 |
|
} |
| 198 |
|
|
| 199 |
+ |
void EAM::setCutoffRadius( RealType rCut ) { |
| 200 |
+ |
eamRcut_ = rCut; |
| 201 |
+ |
haveCutoffRadius_ = true; |
| 202 |
+ |
} |
| 203 |
+ |
|
| 204 |
|
void EAM::initialize() { |
| 205 |
|
|
| 206 |
|
// set up the mixing method: |
| 207 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 208 |
< |
string EAMMixMeth = toUpperCopy(fopts.getEAMMixingMethod()); |
| 209 |
< |
|
| 208 |
> |
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 209 |
> |
toUpper(EAMMixMeth); |
| 210 |
> |
|
| 211 |
|
if (EAMMixMeth == "JOHNSON") |
| 212 |
|
mixMeth_ = eamJohnson; |
| 213 |
|
else if (EAMMixMeth == "DAW") |
| 237 |
|
|
| 238 |
|
if (nbt->isEAM()) { |
| 239 |
|
|
| 240 |
< |
std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 240 |
> |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 241 |
|
|
| 242 |
|
GenericData* data = nbt->getPropertyByName("EAM"); |
| 243 |
|
if (data == NULL) { |
| 288 |
|
// add it to the map: |
| 289 |
|
AtomTypeProperties atp = atomType->getATP(); |
| 290 |
|
|
| 291 |
< |
std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
| 292 |
< |
ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
| 291 |
> |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 292 |
> |
ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 293 |
|
if (ret.second == false) { |
| 294 |
|
sprintf( painCave.errMsg, |
| 295 |
|
"EAM already had a previous entry with ident %d\n", |
| 303 |
|
|
| 304 |
|
// Now, iterate over all known types and add to the mixing map: |
| 305 |
|
|
| 306 |
< |
std::map<AtomType*, EAMAtomData>::iterator it; |
| 306 |
> |
map<AtomType*, EAMAtomData>::iterator it; |
| 307 |
|
for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
| 308 |
|
|
| 309 |
|
AtomType* atype2 = (*it).first; |
| 312 |
|
mixer.phi = getPhi(atomType, atype2); |
| 313 |
|
mixer.explicitlySet = false; |
| 314 |
|
|
| 315 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 316 |
< |
key1 = std::make_pair(atomType, atype2); |
| 317 |
< |
key2 = std::make_pair(atype2, atomType); |
| 315 |
> |
pair<AtomType*, AtomType*> key1, key2; |
| 316 |
> |
key1 = make_pair(atomType, atype2); |
| 317 |
> |
key2 = make_pair(atype2, atomType); |
| 318 |
|
|
| 319 |
|
MixingMap[key1] = mixer; |
| 320 |
|
if (key2 != key1) { |
| 342 |
|
mixer.phi = cs; |
| 343 |
|
mixer.explicitlySet = true; |
| 344 |
|
|
| 345 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 346 |
< |
key1 = std::make_pair(atype1, atype2); |
| 347 |
< |
key2 = std::make_pair(atype2, atype1); |
| 345 |
> |
pair<AtomType*, AtomType*> key1, key2; |
| 346 |
> |
key1 = make_pair(atype1, atype2); |
| 347 |
> |
key2 = make_pair(atype2, atype1); |
| 348 |
|
|
| 349 |
|
MixingMap[key1] = mixer; |
| 350 |
|
if (key2 != key1) { |
| 353 |
|
return; |
| 354 |
|
} |
| 355 |
|
|
| 356 |
< |
void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, |
| 351 |
< |
RealType &rho_i_at_j, RealType &rho_j_at_i) { |
| 356 |
> |
void EAM::calcDensity(InteractionData &idat) { |
| 357 |
|
|
| 358 |
|
if (!initialized_) initialize(); |
| 359 |
|
|
| 360 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 361 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 362 |
< |
|
| 363 |
< |
if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij); |
| 364 |
< |
if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij); |
| 365 |
< |
return; |
| 360 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 361 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 362 |
> |
|
| 363 |
> |
if (haveCutoffRadius_) |
| 364 |
> |
if ( *(idat.rij) > eamRcut_) return; |
| 365 |
> |
|
| 366 |
> |
if ( *(idat.rij) < data1.rcut) |
| 367 |
> |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 368 |
> |
|
| 369 |
> |
|
| 370 |
> |
if ( *(idat.rij) < data2.rcut) |
| 371 |
> |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 372 |
> |
|
| 373 |
> |
return; |
| 374 |
|
} |
| 375 |
< |
|
| 376 |
< |
void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho, |
| 377 |
< |
RealType &dfrhodrho) { |
| 365 |
< |
|
| 375 |
> |
|
| 376 |
> |
void EAM::calcFunctional(SelfData &sdat) { |
| 377 |
> |
|
| 378 |
|
if (!initialized_) initialize(); |
| 379 |
|
|
| 380 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 380 |
> |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 381 |
|
|
| 382 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho); |
| 382 |
> |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 383 |
|
|
| 384 |
< |
frho = result.first; |
| 385 |
< |
dfrhodrho = result.second; |
| 384 |
> |
*(sdat.frho) = result.first; |
| 385 |
> |
*(sdat.dfrhodrho) = result.second; |
| 386 |
> |
|
| 387 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += result.first; |
| 388 |
> |
*(sdat.particlePot) += result.first; |
| 389 |
> |
|
| 390 |
|
return; |
| 391 |
|
} |
| 392 |
|
|
| 393 |
|
|
| 394 |
< |
void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 379 |
< |
RealType rij, RealType r2, RealType sw, |
| 380 |
< |
RealType &vpair, RealType &pot, Vector3d &f1, |
| 381 |
< |
RealType rho_i, RealType rho_j, |
| 382 |
< |
RealType dfrhodrho_i, RealType dfrhodrho_j, |
| 383 |
< |
RealType &fshift_i, RealType &fshift_j) { |
| 394 |
> |
void EAM::calcForce(InteractionData &idat) { |
| 395 |
|
|
| 396 |
|
if (!initialized_) initialize(); |
| 397 |
< |
|
| 397 |
> |
|
| 398 |
> |
if (haveCutoffRadius_) |
| 399 |
> |
if ( *(idat.rij) > eamRcut_) return; |
| 400 |
> |
|
| 401 |
|
pair<RealType, RealType> res; |
| 402 |
|
|
| 403 |
< |
if (rij < eamRcut_) { |
| 404 |
< |
|
| 405 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 406 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 407 |
< |
|
| 408 |
< |
// get type-specific cutoff radii |
| 409 |
< |
|
| 410 |
< |
RealType rci = data1.rcut; |
| 411 |
< |
RealType rcj = data2.rcut; |
| 403 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 404 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 405 |
> |
|
| 406 |
> |
// get type-specific cutoff radii |
| 407 |
> |
|
| 408 |
> |
RealType rci = data1.rcut; |
| 409 |
> |
RealType rcj = data2.rcut; |
| 410 |
> |
|
| 411 |
> |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 412 |
> |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 413 |
> |
RealType phab(0.0), dvpdr(0.0); |
| 414 |
> |
RealType drhoidr, drhojdr, dudr; |
| 415 |
> |
|
| 416 |
> |
if ( *(idat.rij) < rci) { |
| 417 |
> |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 418 |
> |
rha = res.first; |
| 419 |
> |
drha = res.second; |
| 420 |
|
|
| 421 |
< |
RealType rha, drha, rhb, drhb; |
| 422 |
< |
RealType pha, dpha, phb, dphb; |
| 423 |
< |
RealType phab, dvpdr; |
| 424 |
< |
RealType drhoidr, drhojdr, dudr; |
| 421 |
> |
res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 422 |
> |
pha = res.first; |
| 423 |
> |
dpha = res.second; |
| 424 |
> |
} |
| 425 |
> |
|
| 426 |
> |
if ( *(idat.rij) < rcj) { |
| 427 |
> |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 428 |
> |
rhb = res.first; |
| 429 |
> |
drhb = res.second; |
| 430 |
|
|
| 431 |
< |
if (rij < rci) { |
| 432 |
< |
res = data1.rho->getValueAndDerivativeAt(rij); |
| 433 |
< |
rha = res.first; |
| 434 |
< |
drha = res.second; |
| 431 |
> |
res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 432 |
> |
phb = res.first; |
| 433 |
> |
dphb = res.second; |
| 434 |
> |
} |
| 435 |
|
|
| 436 |
< |
res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij); |
| 437 |
< |
pha = res.first; |
| 438 |
< |
dpha = res.second; |
| 436 |
> |
switch(mixMeth_) { |
| 437 |
> |
case eamJohnson: |
| 438 |
> |
|
| 439 |
> |
if ( *(idat.rij) < rci) { |
| 440 |
> |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 441 |
> |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 442 |
> |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 443 |
|
} |
| 444 |
< |
|
| 445 |
< |
if (rij < rcj) { |
| 446 |
< |
res = data2.rho->getValueAndDerivativeAt(rij); |
| 447 |
< |
rhb = res.first; |
| 448 |
< |
drhb = res.second; |
| 449 |
< |
|
| 450 |
< |
res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij); |
| 420 |
< |
phb = res.first; |
| 421 |
< |
dphb = res.second; |
| 422 |
< |
} |
| 423 |
< |
|
| 424 |
< |
phab = 0.0; |
| 425 |
< |
dvpdr = 0.0; |
| 426 |
< |
|
| 427 |
< |
switch(mixMeth_) { |
| 428 |
< |
case eamJohnson: |
| 429 |
< |
|
| 430 |
< |
if (rij < rci) { |
| 431 |
< |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 432 |
< |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 433 |
< |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 434 |
< |
} |
| 435 |
< |
|
| 436 |
< |
if (rij < rcj) { |
| 437 |
< |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 438 |
< |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 439 |
< |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 440 |
< |
} |
| 441 |
< |
|
| 442 |
< |
break; |
| 443 |
< |
|
| 444 |
< |
case eamDaw: |
| 445 |
< |
|
| 446 |
< |
res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij); |
| 447 |
< |
phab = res.first; |
| 448 |
< |
dvpdr = res.second; |
| 449 |
< |
|
| 450 |
< |
break; |
| 451 |
< |
case eamUnknown: |
| 452 |
< |
default: |
| 453 |
< |
|
| 454 |
< |
sprintf(painCave.errMsg, |
| 455 |
< |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 456 |
< |
); |
| 457 |
< |
painCave.severity = OPENMD_ERROR; |
| 458 |
< |
painCave.isFatal = 1; |
| 459 |
< |
simError(); |
| 460 |
< |
|
| 444 |
> |
|
| 445 |
> |
|
| 446 |
> |
|
| 447 |
> |
if ( *(idat.rij) < rcj) { |
| 448 |
> |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 449 |
> |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 450 |
> |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 451 |
|
} |
| 452 |
|
|
| 453 |
< |
drhoidr = drha; |
| 454 |
< |
drhojdr = drhb; |
| 455 |
< |
|
| 456 |
< |
dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr; |
| 457 |
< |
|
| 458 |
< |
f1 = d * dudr / rij; |
| 459 |
< |
|
| 460 |
< |
// particle_pot is the difference between the full potential |
| 461 |
< |
// and the full potential without the presence of a particular |
| 462 |
< |
// particle (atom1). |
| 463 |
< |
// |
| 464 |
< |
// This reduces the density at other particle locations, so |
| 465 |
< |
// we need to recompute the density at atom2 assuming atom1 |
| 466 |
< |
// didn't contribute. This then requires recomputing the |
| 467 |
< |
// density functional for atom2 as well. |
| 468 |
< |
// |
| 469 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 470 |
< |
// pair interaction, and will be handled by vpair. |
| 481 |
< |
|
| 482 |
< |
fshift_i = data1.F->getValueAt( rho_i - rhb ); |
| 483 |
< |
fshift_j = data1.F->getValueAt( rho_j - rha ); |
| 484 |
< |
|
| 485 |
< |
pot += phab; |
| 486 |
< |
|
| 487 |
< |
vpair += phab; |
| 453 |
> |
break; |
| 454 |
> |
|
| 455 |
> |
case eamDaw: |
| 456 |
> |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 457 |
> |
phab = res.first; |
| 458 |
> |
dvpdr = res.second; |
| 459 |
> |
|
| 460 |
> |
break; |
| 461 |
> |
case eamUnknown: |
| 462 |
> |
default: |
| 463 |
> |
|
| 464 |
> |
sprintf(painCave.errMsg, |
| 465 |
> |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 466 |
> |
); |
| 467 |
> |
painCave.severity = OPENMD_ERROR; |
| 468 |
> |
painCave.isFatal = 1; |
| 469 |
> |
simError(); |
| 470 |
> |
|
| 471 |
|
} |
| 489 |
– |
|
| 490 |
– |
return; |
| 472 |
|
|
| 473 |
< |
} |
| 474 |
< |
|
| 494 |
< |
|
| 495 |
< |
void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij, |
| 496 |
< |
RealType* rho_i_at_j, RealType* rho_j_at_i){ |
| 497 |
< |
|
| 498 |
< |
if (!initialized_) initialize(); |
| 473 |
> |
drhoidr = drha; |
| 474 |
> |
drhojdr = drhb; |
| 475 |
|
|
| 476 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 501 |
< |
AtomType* atype2 = EAMlist[*atid2]; |
| 476 |
> |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 477 |
|
|
| 478 |
< |
calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
| 479 |
< |
|
| 480 |
< |
return; |
| 481 |
< |
} |
| 482 |
< |
|
| 483 |
< |
void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho, |
| 484 |
< |
RealType *dfrhodrho) { |
| 485 |
< |
|
| 486 |
< |
if (!initialized_) initialize(); |
| 487 |
< |
|
| 513 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 514 |
< |
|
| 515 |
< |
calcFunctional(atype1, *rho, *frho, *dfrhodrho); |
| 478 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 479 |
> |
|
| 480 |
> |
// particlePot is the difference between the full potential and |
| 481 |
> |
// the full potential without the presence of a particular |
| 482 |
> |
// particle (atom1). |
| 483 |
> |
// |
| 484 |
> |
// This reduces the density at other particle locations, so we |
| 485 |
> |
// need to recompute the density at atom2 assuming atom1 didn't |
| 486 |
> |
// contribute. This then requires recomputing the density |
| 487 |
> |
// functional for atom2 as well. |
| 488 |
|
|
| 489 |
< |
return; |
| 490 |
< |
} |
| 519 |
< |
RealType EAM::getEAMcut(int *atid1) { |
| 520 |
< |
|
| 521 |
< |
if (!initialized_) initialize(); |
| 489 |
> |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 490 |
> |
- *(idat.frho2); |
| 491 |
|
|
| 492 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 493 |
< |
|
| 525 |
< |
return getRcut(atype1); |
| 526 |
< |
} |
| 527 |
< |
|
| 528 |
< |
void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 529 |
< |
RealType *r2, RealType *sw, RealType *vpair, |
| 530 |
< |
RealType *pot, RealType *f1, RealType *rho1, |
| 531 |
< |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 532 |
< |
RealType *fshift1, RealType *fshift2) { |
| 533 |
< |
|
| 534 |
< |
if (!initialized_) initialize(); |
| 492 |
> |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 493 |
> |
- *(idat.frho1); |
| 494 |
|
|
| 495 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 537 |
< |
AtomType* atype2 = EAMlist[*atid2]; |
| 495 |
> |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 496 |
|
|
| 497 |
< |
Vector3d disp(d[0], d[1], d[2]); |
| 498 |
< |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 497 |
> |
*(idat.vpair) += phab; |
| 498 |
> |
|
| 499 |
> |
return; |
| 500 |
|
|
| 542 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair, *pot, frc, |
| 543 |
– |
*rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2); |
| 544 |
– |
|
| 545 |
– |
f1[0] = frc.x(); |
| 546 |
– |
f1[1] = frc.y(); |
| 547 |
– |
f1[2] = frc.z(); |
| 548 |
– |
|
| 549 |
– |
return; |
| 501 |
|
} |
| 551 |
– |
|
| 552 |
– |
void EAM::setCutoffEAM(RealType *thisRcut) { |
| 553 |
– |
eamRcut_ = *thisRcut; |
| 554 |
– |
} |
| 555 |
– |
} |
| 502 |
|
|
| 503 |
< |
extern "C" { |
| 504 |
< |
|
| 559 |
< |
#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO) |
| 560 |
< |
#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO) |
| 561 |
< |
#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR) |
| 562 |
< |
#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM) |
| 563 |
< |
#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT) |
| 503 |
> |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 504 |
> |
if (!initialized_) initialize(); |
| 505 |
|
|
| 506 |
< |
|
| 566 |
< |
void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, |
| 567 |
< |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 568 |
< |
|
| 569 |
< |
return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij, |
| 570 |
< |
rho_i_at_j, |
| 571 |
< |
rho_j_at_i); |
| 572 |
< |
} |
| 573 |
< |
void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, |
| 574 |
< |
RealType *dfrhodrho) { |
| 575 |
< |
|
| 576 |
< |
return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho, |
| 577 |
< |
dfrhodrho); |
| 578 |
< |
|
| 579 |
< |
} |
| 580 |
< |
void fortranSetCutoffEAM(RealType *rcut) { |
| 581 |
< |
return OpenMD::EAM::Instance()->setCutoffEAM(rcut); |
| 582 |
< |
} |
| 583 |
< |
void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 584 |
< |
RealType *r2, RealType *sw, RealType *vpair, |
| 585 |
< |
RealType *pot, RealType *f1, RealType *rho1, |
| 586 |
< |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 587 |
< |
RealType *fshift1, RealType *fshift2){ |
| 588 |
< |
|
| 589 |
< |
return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij, |
| 590 |
< |
r2, sw, vpair, |
| 591 |
< |
pot, f1, rho1, |
| 592 |
< |
rho2, dfrho1, dfrho2, |
| 593 |
< |
fshift1, fshift2); |
| 594 |
< |
} |
| 595 |
< |
RealType fortranGetEAMcut(int* atid) { |
| 596 |
< |
return OpenMD::EAM::Instance()->getEAMcut(atid); |
| 597 |
< |
} |
| 506 |
> |
RealType cut = 0.0; |
| 507 |
|
|
| 508 |
+ |
map<AtomType*, EAMAtomData>::iterator it; |
| 509 |
+ |
|
| 510 |
+ |
it = EAMMap.find(atypes.first); |
| 511 |
+ |
if (it != EAMMap.end()) { |
| 512 |
+ |
EAMAtomData data1 = (*it).second; |
| 513 |
+ |
cut = data1.rcut; |
| 514 |
+ |
} |
| 515 |
+ |
|
| 516 |
+ |
it = EAMMap.find(atypes.second); |
| 517 |
+ |
if (it != EAMMap.end()) { |
| 518 |
+ |
EAMAtomData data2 = (*it).second; |
| 519 |
+ |
if (data2.rcut > cut) |
| 520 |
+ |
cut = data2.rcut; |
| 521 |
+ |
} |
| 522 |
+ |
|
| 523 |
+ |
return cut; |
| 524 |
+ |
} |
| 525 |
|
} |
| 526 |
+ |
|
