| 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> |
| 52 |
|
namespace OpenMD { |
| 53 |
|
|
| 54 |
|
EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), |
| 55 |
< |
mixMeth_(eamJohnson), eamRcut_(0.0) {} |
| 55 |
> |
mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {} |
| 56 |
|
|
| 57 |
< |
EAMParam EAM::getEAMParam(AtomType* atomType) { |
| 58 |
< |
|
| 59 |
< |
// Do sanity checking on the AtomType we were passed before |
| 60 |
< |
// building any data structures: |
| 61 |
< |
if (!atomType->isEAM()) { |
| 61 |
< |
sprintf( painCave.errMsg, |
| 62 |
< |
"EAM::getEAMParam was passed an atomType (%s) that does not\n" |
| 63 |
< |
"\tappear to be an embedded atom method (EAM) atom.\n", |
| 64 |
< |
atomType->getName().c_str()); |
| 65 |
< |
painCave.severity = OPENMD_ERROR; |
| 66 |
< |
painCave.isFatal = 1; |
| 67 |
< |
simError(); |
| 68 |
< |
} |
| 69 |
< |
|
| 70 |
< |
GenericData* data = atomType->getPropertyByName("EAM"); |
| 71 |
< |
if (data == NULL) { |
| 72 |
< |
sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n" |
| 73 |
< |
"\tparameters for atomType %s.\n", |
| 74 |
< |
atomType->getName().c_str()); |
| 75 |
< |
painCave.severity = OPENMD_ERROR; |
| 76 |
< |
painCave.isFatal = 1; |
| 77 |
< |
simError(); |
| 78 |
< |
} |
| 79 |
< |
|
| 80 |
< |
EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
| 81 |
< |
if (eamData == NULL) { |
| 82 |
< |
sprintf( painCave.errMsg, |
| 83 |
< |
"EAM::getEAMParam could not convert GenericData to EAMParam for\n" |
| 84 |
< |
"\tatom type %s\n", atomType->getName().c_str()); |
| 85 |
< |
painCave.severity = OPENMD_ERROR; |
| 86 |
< |
painCave.isFatal = 1; |
| 87 |
< |
simError(); |
| 88 |
< |
} |
| 89 |
< |
|
| 90 |
< |
return eamData->getData(); |
| 91 |
< |
} |
| 57 |
> |
CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { |
| 58 |
> |
EAMAdapter ea1 = EAMAdapter(atomType1); |
| 59 |
> |
EAMAdapter ea2 = EAMAdapter(atomType2); |
| 60 |
> |
CubicSpline* z1 = ea1.getZ(); |
| 61 |
> |
CubicSpline* z2 = ea2.getZ(); |
| 62 |
|
|
| 93 |
– |
CubicSpline* EAM::getZ(AtomType* atomType) { |
| 94 |
– |
EAMParam eamParam = getEAMParam(atomType); |
| 95 |
– |
int nr = eamParam.nr; |
| 96 |
– |
RealType dr = eamParam.dr; |
| 97 |
– |
vector<RealType> rvals; |
| 98 |
– |
|
| 99 |
– |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
| 100 |
– |
|
| 101 |
– |
CubicSpline* cs = new CubicSpline(); |
| 102 |
– |
cs->addPoints(rvals, eamParam.Z); |
| 103 |
– |
return cs; |
| 104 |
– |
} |
| 105 |
– |
|
| 106 |
– |
RealType EAM::getRcut(AtomType* atomType) { |
| 107 |
– |
EAMParam eamParam = getEAMParam(atomType); |
| 108 |
– |
return eamParam.rcut; |
| 109 |
– |
} |
| 110 |
– |
|
| 111 |
– |
CubicSpline* EAM::getRho(AtomType* atomType) { |
| 112 |
– |
EAMParam eamParam = getEAMParam(atomType); |
| 113 |
– |
int nr = eamParam.nr; |
| 114 |
– |
RealType dr = eamParam.dr; |
| 115 |
– |
vector<RealType> rvals; |
| 116 |
– |
|
| 117 |
– |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr); |
| 118 |
– |
|
| 119 |
– |
CubicSpline* cs = new CubicSpline(); |
| 120 |
– |
cs->addPoints(rvals, eamParam.rho); |
| 121 |
– |
return cs; |
| 122 |
– |
} |
| 123 |
– |
|
| 124 |
– |
CubicSpline* EAM::getF(AtomType* atomType) { |
| 125 |
– |
EAMParam eamParam = getEAMParam(atomType); |
| 126 |
– |
int nrho = eamParam.nrho; |
| 127 |
– |
RealType drho = eamParam.drho; |
| 128 |
– |
vector<RealType> rhovals; |
| 129 |
– |
vector<RealType> scaledF; |
| 130 |
– |
|
| 131 |
– |
for (int i = 0; i < nrho; i++) { |
| 132 |
– |
rhovals.push_back(RealType(i) * drho); |
| 133 |
– |
scaledF.push_back( eamParam.F[i] * 23.06054 ); |
| 134 |
– |
} |
| 135 |
– |
|
| 136 |
– |
CubicSpline* cs = new CubicSpline(); |
| 137 |
– |
cs->addPoints(rhovals, scaledF); |
| 138 |
– |
return cs; |
| 139 |
– |
} |
| 140 |
– |
|
| 141 |
– |
CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { |
| 142 |
– |
EAMParam eamParam1 = getEAMParam(atomType1); |
| 143 |
– |
EAMParam eamParam2 = getEAMParam(atomType2); |
| 144 |
– |
CubicSpline* z1 = getZ(atomType1); |
| 145 |
– |
CubicSpline* z2 = getZ(atomType2); |
| 146 |
– |
|
| 63 |
|
// make the r grid: |
| 64 |
|
|
| 65 |
|
|
| 66 |
|
// we need phi out to the largest value we'll encounter in the radial space; |
| 67 |
|
|
| 68 |
|
RealType rmax = 0.0; |
| 69 |
< |
rmax = max(rmax, eamParam1.rcut); |
| 70 |
< |
rmax = max(rmax, eamParam1.nr * eamParam1.dr); |
| 69 |
> |
rmax = max(rmax, ea1.getRcut()); |
| 70 |
> |
rmax = max(rmax, ea1.getNr() * ea1.getDr()); |
| 71 |
|
|
| 72 |
< |
rmax = max(rmax, eamParam2.rcut); |
| 73 |
< |
rmax = max(rmax, eamParam2.nr * eamParam2.dr); |
| 72 |
> |
rmax = max(rmax, ea2.getRcut()); |
| 73 |
> |
rmax = max(rmax, ea2.getNr() * ea2.getDr()); |
| 74 |
|
|
| 75 |
|
// use the smallest dr (finest grid) to build our grid: |
| 76 |
|
|
| 77 |
< |
RealType dr = min(eamParam1.dr, eamParam2.dr); |
| 77 |
> |
RealType dr = min(ea1.getDr(), ea2.getDr()); |
| 78 |
|
|
| 79 |
|
int nr = int(rmax/dr + 0.5); |
| 80 |
|
|
| 98 |
|
// means that our phi grid goes out beyond the cutoff of the |
| 99 |
|
// pair potential |
| 100 |
|
|
| 101 |
< |
zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0; |
| 102 |
< |
zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0; |
| 101 |
> |
zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0; |
| 102 |
> |
zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0; |
| 103 |
|
|
| 104 |
|
phi = 331.999296 * (zi * zj) / r; |
| 105 |
|
|
| 111 |
|
return cs; |
| 112 |
|
} |
| 113 |
|
|
| 114 |
+ |
void EAM::setCutoffRadius( RealType rCut ) { |
| 115 |
+ |
eamRcut_ = rCut; |
| 116 |
+ |
haveCutoffRadius_ = true; |
| 117 |
+ |
} |
| 118 |
+ |
|
| 119 |
|
void EAM::initialize() { |
| 120 |
|
|
| 121 |
|
// set up the mixing method: |
| 193 |
|
|
| 194 |
|
void EAM::addType(AtomType* atomType){ |
| 195 |
|
|
| 196 |
+ |
EAMAdapter ea = EAMAdapter(atomType); |
| 197 |
|
EAMAtomData eamAtomData; |
| 276 |
– |
|
| 277 |
– |
eamAtomData.rho = getRho(atomType); |
| 278 |
– |
eamAtomData.F = getF(atomType); |
| 279 |
– |
eamAtomData.Z = getZ(atomType); |
| 280 |
– |
eamAtomData.rcut = getRcut(atomType); |
| 198 |
|
|
| 199 |
+ |
eamAtomData.rho = ea.getRho(); |
| 200 |
+ |
eamAtomData.F = ea.getF(); |
| 201 |
+ |
eamAtomData.Z = ea.getZ(); |
| 202 |
+ |
eamAtomData.rcut = ea.getRcut(); |
| 203 |
+ |
|
| 204 |
|
// add it to the map: |
| 283 |
– |
AtomTypeProperties atp = atomType->getATP(); |
| 205 |
|
|
| 206 |
|
pair<map<int,AtomType*>::iterator,bool> ret; |
| 207 |
< |
ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 207 |
> |
ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
| 208 |
|
if (ret.second == false) { |
| 209 |
|
sprintf( painCave.errMsg, |
| 210 |
|
"EAM already had a previous entry with ident %d\n", |
| 211 |
< |
atp.ident); |
| 211 |
> |
atomType->getIdent()); |
| 212 |
|
painCave.severity = OPENMD_INFO; |
| 213 |
|
painCave.isFatal = 0; |
| 214 |
|
simError(); |
| 268 |
|
return; |
| 269 |
|
} |
| 270 |
|
|
| 271 |
< |
void EAM::calcDensity(DensityData ddat) { |
| 271 |
> |
void EAM::calcDensity(InteractionData &idat) { |
| 272 |
|
|
| 273 |
|
if (!initialized_) initialize(); |
| 274 |
|
|
| 275 |
< |
EAMAtomData data1 = EAMMap[ddat.atype1]; |
| 276 |
< |
EAMAtomData data2 = EAMMap[ddat.atype2]; |
| 277 |
< |
|
| 278 |
< |
if (ddat.rij < data1.rcut) |
| 279 |
< |
ddat.rho_i_at_j = data1.rho->getValueAt(ddat.rij); |
| 280 |
< |
|
| 281 |
< |
if (ddat.rij < data2.rcut) |
| 282 |
< |
ddat.rho_j_at_i = data2.rho->getValueAt(ddat.rij); |
| 283 |
< |
|
| 284 |
< |
return; |
| 275 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 276 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 277 |
> |
|
| 278 |
> |
if (haveCutoffRadius_) |
| 279 |
> |
if ( *(idat.rij) > eamRcut_) return; |
| 280 |
> |
|
| 281 |
> |
if ( *(idat.rij) < data1.rcut) |
| 282 |
> |
*(idat.rho1) += data1.rho->getValueAt( *(idat.rij)); |
| 283 |
> |
|
| 284 |
> |
|
| 285 |
> |
if ( *(idat.rij) < data2.rcut) |
| 286 |
> |
*(idat.rho2) += data2.rho->getValueAt( *(idat.rij)); |
| 287 |
> |
|
| 288 |
> |
return; |
| 289 |
|
} |
| 290 |
< |
|
| 291 |
< |
void EAM::calcFunctional(FunctionalData fdat) { |
| 292 |
< |
|
| 290 |
> |
|
| 291 |
> |
void EAM::calcFunctional(SelfData &sdat) { |
| 292 |
> |
|
| 293 |
|
if (!initialized_) initialize(); |
| 294 |
|
|
| 295 |
< |
EAMAtomData data1 = EAMMap[fdat.atype]; |
| 295 |
> |
EAMAtomData data1 = EAMMap[ sdat.atype ]; |
| 296 |
|
|
| 297 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(fdat.rho); |
| 297 |
> |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) ); |
| 298 |
|
|
| 299 |
< |
fdat.frho = result.first; |
| 300 |
< |
fdat.dfrhodrho = result.second; |
| 299 |
> |
*(sdat.frho) = result.first; |
| 300 |
> |
*(sdat.dfrhodrho) = result.second; |
| 301 |
> |
|
| 302 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += result.first; |
| 303 |
> |
*(sdat.particlePot) += result.first; |
| 304 |
> |
|
| 305 |
|
return; |
| 306 |
|
} |
| 307 |
|
|
| 308 |
|
|
| 309 |
< |
void EAM::calcForce(InteractionData idat) { |
| 309 |
> |
void EAM::calcForce(InteractionData &idat) { |
| 310 |
|
|
| 311 |
|
if (!initialized_) initialize(); |
| 312 |
|
|
| 313 |
+ |
if (haveCutoffRadius_) |
| 314 |
+ |
if ( *(idat.rij) > eamRcut_) return; |
| 315 |
+ |
|
| 316 |
|
pair<RealType, RealType> res; |
| 317 |
|
|
| 318 |
< |
if (idat.rij < eamRcut_) { |
| 319 |
< |
|
| 320 |
< |
EAMAtomData data1 = EAMMap[idat.atype1]; |
| 321 |
< |
EAMAtomData data2 = EAMMap[idat.atype2]; |
| 322 |
< |
|
| 323 |
< |
// get type-specific cutoff radii |
| 324 |
< |
|
| 325 |
< |
RealType rci = data1.rcut; |
| 326 |
< |
RealType rcj = data2.rcut; |
| 318 |
> |
EAMAtomData data1 = EAMMap[idat.atypes.first]; |
| 319 |
> |
EAMAtomData data2 = EAMMap[idat.atypes.second]; |
| 320 |
> |
|
| 321 |
> |
// get type-specific cutoff radii |
| 322 |
> |
|
| 323 |
> |
RealType rci = data1.rcut; |
| 324 |
> |
RealType rcj = data2.rcut; |
| 325 |
> |
|
| 326 |
> |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 327 |
> |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 328 |
> |
RealType phab(0.0), dvpdr(0.0); |
| 329 |
> |
RealType drhoidr, drhojdr, dudr; |
| 330 |
> |
|
| 331 |
> |
if ( *(idat.rij) < rci) { |
| 332 |
> |
res = data1.rho->getValueAndDerivativeAt( *(idat.rij)); |
| 333 |
> |
rha = res.first; |
| 334 |
> |
drha = res.second; |
| 335 |
|
|
| 336 |
< |
RealType rha, drha, rhb, drhb; |
| 337 |
< |
RealType pha, dpha, phb, dphb; |
| 338 |
< |
RealType phab, dvpdr; |
| 339 |
< |
RealType drhoidr, drhojdr, dudr; |
| 336 |
> |
res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 337 |
> |
pha = res.first; |
| 338 |
> |
dpha = res.second; |
| 339 |
> |
} |
| 340 |
> |
|
| 341 |
> |
if ( *(idat.rij) < rcj) { |
| 342 |
> |
res = data2.rho->getValueAndDerivativeAt( *(idat.rij) ); |
| 343 |
> |
rhb = res.first; |
| 344 |
> |
drhb = res.second; |
| 345 |
|
|
| 346 |
< |
if (idat.rij < rci) { |
| 347 |
< |
res = data1.rho->getValueAndDerivativeAt(idat.rij); |
| 348 |
< |
rha = res.first; |
| 349 |
< |
drha = res.second; |
| 346 |
> |
res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) ); |
| 347 |
> |
phb = res.first; |
| 348 |
> |
dphb = res.second; |
| 349 |
> |
} |
| 350 |
|
|
| 351 |
< |
res = MixingMap[make_pair(idat.atype1, idat.atype1)].phi->getValueAndDerivativeAt(idat.rij); |
| 352 |
< |
pha = res.first; |
| 353 |
< |
dpha = res.second; |
| 351 |
> |
switch(mixMeth_) { |
| 352 |
> |
case eamJohnson: |
| 353 |
> |
|
| 354 |
> |
if ( *(idat.rij) < rci) { |
| 355 |
> |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 356 |
> |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 357 |
> |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 358 |
|
} |
| 359 |
< |
|
| 360 |
< |
if (idat.rij < rcj) { |
| 361 |
< |
res = data2.rho->getValueAndDerivativeAt(idat.rij); |
| 362 |
< |
rhb = res.first; |
| 363 |
< |
drhb = res.second; |
| 364 |
< |
|
| 365 |
< |
res = MixingMap[make_pair(idat.atype2, idat.atype2)].phi->getValueAndDerivativeAt(idat.rij); |
| 417 |
< |
phb = res.first; |
| 418 |
< |
dphb = res.second; |
| 359 |
> |
|
| 360 |
> |
|
| 361 |
> |
|
| 362 |
> |
if ( *(idat.rij) < rcj) { |
| 363 |
> |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 364 |
> |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 365 |
> |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 366 |
|
} |
| 420 |
– |
|
| 421 |
– |
phab = 0.0; |
| 422 |
– |
dvpdr = 0.0; |
| 423 |
– |
|
| 424 |
– |
switch(mixMeth_) { |
| 425 |
– |
case eamJohnson: |
| 426 |
– |
|
| 427 |
– |
if (idat.rij < rci) { |
| 428 |
– |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 429 |
– |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 430 |
– |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 431 |
– |
} |
| 432 |
– |
|
| 433 |
– |
if (idat.rij < rcj) { |
| 434 |
– |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 435 |
– |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 436 |
– |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 437 |
– |
} |
| 438 |
– |
|
| 439 |
– |
break; |
| 440 |
– |
|
| 441 |
– |
case eamDaw: |
| 442 |
– |
res = MixingMap[make_pair(idat.atype1,idat.atype2)].phi->getValueAndDerivativeAt(idat.rij); |
| 443 |
– |
phab = res.first; |
| 444 |
– |
dvpdr = res.second; |
| 445 |
– |
|
| 446 |
– |
break; |
| 447 |
– |
case eamUnknown: |
| 448 |
– |
default: |
| 449 |
– |
|
| 450 |
– |
sprintf(painCave.errMsg, |
| 451 |
– |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 452 |
– |
); |
| 453 |
– |
painCave.severity = OPENMD_ERROR; |
| 454 |
– |
painCave.isFatal = 1; |
| 455 |
– |
simError(); |
| 456 |
– |
|
| 457 |
– |
} |
| 367 |
|
|
| 368 |
< |
drhoidr = drha; |
| 369 |
< |
drhojdr = drhb; |
| 370 |
< |
|
| 371 |
< |
dudr = drhojdr*idat.dfrho1 + drhoidr*idat.dfrho2 + dvpdr; |
| 372 |
< |
|
| 373 |
< |
idat.f1 = idat.d * dudr / idat.rij; |
| 374 |
< |
|
| 375 |
< |
// particle_pot is the difference between the full potential |
| 376 |
< |
// and the full potential without the presence of a particular |
| 377 |
< |
// particle (atom1). |
| 378 |
< |
// |
| 379 |
< |
// This reduces the density at other particle locations, so |
| 380 |
< |
// we need to recompute the density at atom2 assuming atom1 |
| 381 |
< |
// didn't contribute. This then requires recomputing the |
| 382 |
< |
// density functional for atom2 as well. |
| 383 |
< |
// |
| 384 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 385 |
< |
// pair interaction, and will be handled by vpair. |
| 477 |
< |
|
| 478 |
< |
idat.fshift1 = data1.F->getValueAt( idat.rho1 - rhb ); |
| 479 |
< |
idat.fshift2 = data1.F->getValueAt( idat.rho2 - rha ); |
| 480 |
< |
|
| 481 |
< |
idat.pot += phab; |
| 482 |
< |
|
| 483 |
< |
idat.vpair += phab; |
| 368 |
> |
break; |
| 369 |
> |
|
| 370 |
> |
case eamDaw: |
| 371 |
> |
res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij)); |
| 372 |
> |
phab = res.first; |
| 373 |
> |
dvpdr = res.second; |
| 374 |
> |
|
| 375 |
> |
break; |
| 376 |
> |
case eamUnknown: |
| 377 |
> |
default: |
| 378 |
> |
|
| 379 |
> |
sprintf(painCave.errMsg, |
| 380 |
> |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 381 |
> |
); |
| 382 |
> |
painCave.severity = OPENMD_ERROR; |
| 383 |
> |
painCave.isFatal = 1; |
| 384 |
> |
simError(); |
| 385 |
> |
|
| 386 |
|
} |
| 387 |
< |
|
| 387 |
> |
|
| 388 |
> |
drhoidr = drha; |
| 389 |
> |
drhojdr = drhb; |
| 390 |
> |
|
| 391 |
> |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 392 |
> |
|
| 393 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 394 |
> |
|
| 395 |
> |
// particlePot is the difference between the full potential and |
| 396 |
> |
// the full potential without the presence of a particular |
| 397 |
> |
// particle (atom1). |
| 398 |
> |
// |
| 399 |
> |
// This reduces the density at other particle locations, so we |
| 400 |
> |
// need to recompute the density at atom2 assuming atom1 didn't |
| 401 |
> |
// contribute. This then requires recomputing the density |
| 402 |
> |
// functional for atom2 as well. |
| 403 |
> |
|
| 404 |
> |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 405 |
> |
- *(idat.frho2); |
| 406 |
> |
|
| 407 |
> |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 408 |
> |
- *(idat.frho1); |
| 409 |
> |
|
| 410 |
> |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 411 |
> |
|
| 412 |
> |
*(idat.vpair) += phab; |
| 413 |
> |
|
| 414 |
|
return; |
| 415 |
|
|
| 416 |
|
} |
| 417 |
|
|
| 418 |
< |
RealType EAM::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 418 |
> |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 419 |
|
if (!initialized_) initialize(); |
| 420 |
|
|
| 421 |
|
RealType cut = 0.0; |
| 422 |
|
|
| 423 |
|
map<AtomType*, EAMAtomData>::iterator it; |
| 424 |
|
|
| 425 |
< |
it = EAMMap.find(at1); |
| 425 |
> |
it = EAMMap.find(atypes.first); |
| 426 |
|
if (it != EAMMap.end()) { |
| 427 |
|
EAMAtomData data1 = (*it).second; |
| 428 |
|
cut = data1.rcut; |
| 429 |
|
} |
| 430 |
|
|
| 431 |
< |
it = EAMMap.find(at2); |
| 431 |
> |
it = EAMMap.find(atypes.second); |
| 432 |
|
if (it != EAMMap.end()) { |
| 433 |
|
EAMAtomData data2 = (*it).second; |
| 434 |
|
if (data2.rcut > cut) |
