| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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 |
|
|
| 57 |
< |
EAM* EAM::_instance = NULL; |
| 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 |
|
|
| 63 |
< |
EAM* EAM::Instance() { |
| 64 |
< |
if (!_instance) { |
| 65 |
< |
_instance = new EAM(); |
| 66 |
< |
} |
| 67 |
< |
return _instance; |
| 69 |
< |
} |
| 70 |
< |
|
| 71 |
< |
EAMParam EAM::getEAMParam(AtomType* atomType) { |
| 72 |
< |
|
| 73 |
< |
// Do sanity checking on the AtomType we were passed before |
| 74 |
< |
// building any data structures: |
| 75 |
< |
if (!atomType->isEAM()) { |
| 76 |
< |
sprintf( painCave.errMsg, |
| 77 |
< |
"EAM::getEAMParam was passed an atomType (%s) that does not\n" |
| 78 |
< |
"\tappear to be an embedded atom method (EAM) atom.\n", |
| 79 |
< |
atomType->getName().c_str()); |
| 80 |
< |
painCave.severity = OPENMD_ERROR; |
| 81 |
< |
painCave.isFatal = 1; |
| 82 |
< |
simError(); |
| 83 |
< |
} |
| 84 |
< |
|
| 85 |
< |
GenericData* data = atomType->getPropertyByName("EAM"); |
| 86 |
< |
if (data == NULL) { |
| 87 |
< |
sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n" |
| 88 |
< |
"\tparameters for atomType %s.\n", |
| 89 |
< |
atomType->getName().c_str()); |
| 90 |
< |
painCave.severity = OPENMD_ERROR; |
| 91 |
< |
painCave.isFatal = 1; |
| 92 |
< |
simError(); |
| 93 |
< |
} |
| 94 |
< |
|
| 95 |
< |
EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
| 96 |
< |
if (eamData == NULL) { |
| 97 |
< |
sprintf( painCave.errMsg, |
| 98 |
< |
"EAM::getEAMParam could not convert GenericData to EAMParam for\n" |
| 99 |
< |
"\tatom type %s\n", atomType->getName().c_str()); |
| 100 |
< |
painCave.severity = OPENMD_ERROR; |
| 101 |
< |
painCave.isFatal = 1; |
| 102 |
< |
simError(); |
| 103 |
< |
} |
| 104 |
< |
|
| 105 |
< |
return eamData->getData(); |
| 106 |
< |
} |
| 63 |
> |
// Thise prefactors convert the charge-charge interactions into |
| 64 |
> |
// kcal / mol all were computed assuming distances are measured in |
| 65 |
> |
// angstroms Charge-Charge, assuming charges are measured in |
| 66 |
> |
// electrons. Matches value in Electrostatics.cpp |
| 67 |
> |
pre11_ = 332.0637778; |
| 68 |
|
|
| 69 |
< |
CubicSpline* EAM::getZ(AtomType* atomType) { |
| 109 |
< |
EAMParam eamParam = getEAMParam(atomType); |
| 110 |
< |
int nr = eamParam.nr; |
| 111 |
< |
RealType dr = eamParam.dr; |
| 112 |
< |
vector<RealType> rvals; |
| 113 |
< |
|
| 114 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i * dr); |
| 115 |
< |
|
| 116 |
< |
CubicSpline* cs = new CubicSpline(); |
| 117 |
< |
cs->addPoints(rvals, eamParam.Z); |
| 118 |
< |
return cs; |
| 119 |
< |
} |
| 69 |
> |
// make the r grid: |
| 70 |
|
|
| 71 |
< |
RealType EAM::getRcut(AtomType* atomType) { |
| 122 |
< |
EAMParam eamParam = getEAMParam(atomType); |
| 123 |
< |
return eamParam.rcut; |
| 124 |
< |
} |
| 125 |
< |
|
| 126 |
< |
CubicSpline* EAM::getRho(AtomType* atomType) { |
| 127 |
< |
EAMParam eamParam = getEAMParam(atomType); |
| 128 |
< |
int nr = eamParam.nr; |
| 129 |
< |
RealType dr = eamParam.dr; |
| 130 |
< |
vector<RealType> rvals; |
| 71 |
> |
// we need phi out to the largest value we'll encounter in the radial space; |
| 72 |
|
|
| 73 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i * dr); |
| 74 |
< |
|
| 75 |
< |
CubicSpline* cs = new CubicSpline(); |
| 135 |
< |
cs->addPoints(rvals, eamParam.rho); |
| 136 |
< |
return cs; |
| 137 |
< |
} |
| 73 |
> |
RealType rmax = 0.0; |
| 74 |
> |
rmax = max(rmax, ea1.getRcut()); |
| 75 |
> |
rmax = max(rmax, ea1.getNr() * ea1.getDr()); |
| 76 |
|
|
| 77 |
< |
CubicSpline* EAM::getF(AtomType* atomType) { |
| 78 |
< |
EAMParam eamParam = getEAMParam(atomType); |
| 141 |
< |
int nrho = eamParam.nrho; |
| 142 |
< |
RealType drho = eamParam.drho; |
| 143 |
< |
vector<RealType> rhovals; |
| 144 |
< |
vector<RealType> scaledF; |
| 145 |
< |
|
| 146 |
< |
for (int i = 0; i < nrho; i++) { |
| 147 |
< |
rhovals.push_back(i * drho); |
| 148 |
< |
scaledF.push_back( eamParam.F[i] * 23.06054 ); |
| 149 |
< |
} |
| 150 |
< |
|
| 151 |
< |
CubicSpline* cs = new CubicSpline(); |
| 152 |
< |
cs->addPoints(rhovals, eamParam.F); |
| 153 |
< |
return cs; |
| 154 |
< |
} |
| 155 |
< |
|
| 156 |
< |
CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { |
| 157 |
< |
EAMParam eamParam1 = getEAMParam(atomType1); |
| 158 |
< |
EAMParam eamParam2 = getEAMParam(atomType2); |
| 159 |
< |
CubicSpline* z1 = getZ(atomType1); |
| 160 |
< |
CubicSpline* z2 = getZ(atomType2); |
| 77 |
> |
rmax = max(rmax, ea2.getRcut()); |
| 78 |
> |
rmax = max(rmax, ea2.getNr() * ea2.getDr()); |
| 79 |
|
|
| 80 |
< |
// make the r grid: |
| 80 |
> |
// use the smallest dr (finest grid) to build our grid: |
| 81 |
|
|
| 82 |
< |
// set rcut to be the smaller of the two atomic rcuts |
| 82 |
> |
RealType dr = min(ea1.getDr(), ea2.getDr()); |
| 83 |
|
|
| 84 |
< |
RealType rcut = eamParam1.rcut < eamParam2.rcut ? |
| 167 |
< |
eamParam1.rcut : eamParam2.rcut; |
| 84 |
> |
int nr = int(rmax/dr + 0.5); |
| 85 |
|
|
| 169 |
– |
// use the smallest dr (finest grid) to build our grid: |
| 170 |
– |
|
| 171 |
– |
RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr; |
| 172 |
– |
int nr = int(rcut/dr); |
| 86 |
|
vector<RealType> rvals; |
| 87 |
< |
for (int i = 0; i < nr; i++) rvals.push_back(i*dr); |
| 87 |
> |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); |
| 88 |
|
|
| 89 |
|
// construct the pair potential: |
| 90 |
|
|
| 95 |
|
|
| 96 |
|
phivals.push_back(0.0); |
| 97 |
|
|
| 98 |
< |
for (int i = 1; i < rvals.size(); i++ ) { |
| 98 |
> |
for (unsigned int i = 1; i < rvals.size(); i++ ) { |
| 99 |
|
r = rvals[i]; |
| 187 |
– |
zi = z1->getValueAt(r); |
| 188 |
– |
zj = z2->getValueAt(r); |
| 100 |
|
|
| 101 |
< |
phi = 331.999296 * (zi * zj) / r; |
| 101 |
> |
// only use z(r) if we're inside this atom's cutoff radius, |
| 102 |
> |
// otherwise, we'll use zero for the charge. This effectively |
| 103 |
> |
// means that our phi grid goes out beyond the cutoff of the |
| 104 |
> |
// pair potential |
| 105 |
> |
|
| 106 |
> |
zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0; |
| 107 |
> |
zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0; |
| 108 |
> |
|
| 109 |
> |
phi = pre11_ * (zi * zj) / r; |
| 110 |
> |
|
| 111 |
|
phivals.push_back(phi); |
| 112 |
|
} |
| 113 |
|
|
| 116 |
|
return cs; |
| 117 |
|
} |
| 118 |
|
|
| 119 |
< |
void EAM::initialize() { |
| 119 |
> |
void EAM::setCutoffRadius( RealType rCut ) { |
| 120 |
> |
eamRcut_ = rCut; |
| 121 |
> |
haveCutoffRadius_ = true; |
| 122 |
> |
} |
| 123 |
|
|
| 124 |
+ |
void EAM::initialize() { |
| 125 |
|
// set up the mixing method: |
| 126 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 127 |
< |
std::string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 127 |
> |
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 128 |
|
toUpper(EAMMixMeth); |
| 129 |
|
|
| 130 |
|
if (EAMMixMeth == "JOHNSON") |
| 135 |
|
mixMeth_ = eamUnknown; |
| 136 |
|
|
| 137 |
|
// find all of the EAM atom Types: |
| 138 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 139 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 140 |
< |
AtomType* at; |
| 138 |
> |
EAMtypes.clear(); |
| 139 |
> |
EAMtids.clear(); |
| 140 |
> |
EAMdata.clear(); |
| 141 |
> |
MixingMap.clear(); |
| 142 |
> |
nEAM_ = 0; |
| 143 |
> |
|
| 144 |
> |
EAMtids.resize( forceField_->getNAtomType(), -1); |
| 145 |
|
|
| 146 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 147 |
< |
at = atomTypes->nextType(i)) { |
| 148 |
< |
|
| 221 |
< |
if (at->isEAM()) |
| 222 |
< |
addType(at); |
| 146 |
> |
set<AtomType*>::iterator at; |
| 147 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 148 |
> |
if ((*at)->isEAM()) nEAM_++; |
| 149 |
|
} |
| 150 |
+ |
EAMdata.resize(nEAM_); |
| 151 |
+ |
MixingMap.resize(nEAM_); |
| 152 |
+ |
|
| 153 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 154 |
+ |
if ((*at)->isEAM()) addType(*at); |
| 155 |
+ |
} |
| 156 |
|
|
| 157 |
|
// find all of the explicit EAM interactions (setfl): |
| 158 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 164 |
|
|
| 165 |
|
if (nbt->isEAM()) { |
| 166 |
|
|
| 167 |
< |
std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 167 |
> |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 168 |
|
|
| 169 |
|
GenericData* data = nbt->getPropertyByName("EAM"); |
| 170 |
|
if (data == NULL) { |
| 205 |
|
|
| 206 |
|
void EAM::addType(AtomType* atomType){ |
| 207 |
|
|
| 208 |
+ |
EAMAdapter ea = EAMAdapter(atomType); |
| 209 |
|
EAMAtomData eamAtomData; |
| 277 |
– |
|
| 278 |
– |
eamAtomData.rho = getRho(atomType); |
| 279 |
– |
eamAtomData.F = getF(atomType); |
| 280 |
– |
eamAtomData.Z = getZ(atomType); |
| 281 |
– |
eamAtomData.rcut = getRcut(atomType); |
| 210 |
|
|
| 211 |
+ |
eamAtomData.rho = ea.getRho(); |
| 212 |
+ |
eamAtomData.F = ea.getF(); |
| 213 |
+ |
eamAtomData.Z = ea.getZ(); |
| 214 |
+ |
eamAtomData.rcut = ea.getRcut(); |
| 215 |
+ |
eamAtomData.isFluctuating = atomType->isFluctuatingCharge(); |
| 216 |
+ |
|
| 217 |
|
// add it to the map: |
| 218 |
< |
AtomTypeProperties atp = atomType->getATP(); |
| 218 |
> |
int atid = atomType->getIdent(); |
| 219 |
> |
int eamtid = EAMtypes.size(); |
| 220 |
|
|
| 221 |
< |
std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
| 222 |
< |
ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
| 221 |
> |
pair<set<int>::iterator,bool> ret; |
| 222 |
> |
ret = EAMtypes.insert( atid ); |
| 223 |
|
if (ret.second == false) { |
| 224 |
|
sprintf( painCave.errMsg, |
| 225 |
|
"EAM already had a previous entry with ident %d\n", |
| 226 |
< |
atp.ident); |
| 226 |
> |
atid); |
| 227 |
|
painCave.severity = OPENMD_INFO; |
| 228 |
|
painCave.isFatal = 0; |
| 229 |
|
simError(); |
| 230 |
|
} |
| 231 |
|
|
| 232 |
< |
EAMMap[atomType] = eamAtomData; |
| 232 |
> |
if (eamAtomData.isFluctuating) { |
| 233 |
> |
// compute charge to rho scaling: |
| 234 |
> |
RealType z0 = eamAtomData.Z->getValueAt(0.0); |
| 235 |
> |
RealType dr = ea.getDr(); |
| 236 |
> |
RealType rmax = max(eamAtomData.rcut, ea.getNr() * dr); |
| 237 |
> |
int nr = int(rmax/dr + 0.5); |
| 238 |
> |
RealType r; |
| 239 |
> |
RealType sum(0.0); |
| 240 |
> |
|
| 241 |
> |
for (int i = 0; i < nr; i++) { |
| 242 |
> |
r = RealType(i*dr); |
| 243 |
> |
sum += r * r * eamAtomData.rho->getValueAt(r) * dr; |
| 244 |
> |
} |
| 245 |
> |
sum *= 4.0 * M_PI; |
| 246 |
> |
eamAtomData.qToRhoScaling = sum / z0; |
| 247 |
> |
} |
| 248 |
> |
|
| 249 |
> |
|
| 250 |
> |
EAMtids[atid] = eamtid; |
| 251 |
> |
EAMdata[eamtid] = eamAtomData; |
| 252 |
> |
MixingMap[eamtid].resize(nEAM_); |
| 253 |
|
|
| 254 |
|
// Now, iterate over all known types and add to the mixing map: |
| 255 |
|
|
| 256 |
< |
std::map<AtomType*, EAMAtomData>::iterator it; |
| 257 |
< |
for( it = EAMMap.begin(); it != EAMMap.end(); ++it) { |
| 256 |
> |
std::set<int>::iterator it; |
| 257 |
> |
for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) { |
| 258 |
|
|
| 259 |
< |
AtomType* atype2 = (*it).first; |
| 259 |
> |
int eamtid2 = EAMtids[ (*it) ]; |
| 260 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 261 |
|
|
| 262 |
|
EAMInteractionData mixer; |
| 263 |
|
mixer.phi = getPhi(atomType, atype2); |
| 264 |
|
mixer.explicitlySet = false; |
| 265 |
|
|
| 266 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 311 |
< |
key1 = std::make_pair(atomType, atype2); |
| 312 |
< |
key2 = std::make_pair(atype2, atomType); |
| 266 |
> |
MixingMap[eamtid2].resize( nEAM_ ); |
| 267 |
|
|
| 268 |
< |
MixingMap[key1] = mixer; |
| 269 |
< |
if (key2 != key1) { |
| 270 |
< |
MixingMap[key2] = mixer; |
| 268 |
> |
MixingMap[eamtid][eamtid2] = mixer; |
| 269 |
> |
if (eamtid2 != eamtid) { |
| 270 |
> |
MixingMap[eamtid2][eamtid] = mixer; |
| 271 |
|
} |
| 272 |
|
} |
| 273 |
|
return; |
| 291 |
|
mixer.phi = cs; |
| 292 |
|
mixer.explicitlySet = true; |
| 293 |
|
|
| 294 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 295 |
< |
key1 = std::make_pair(atype1, atype2); |
| 342 |
< |
key2 = std::make_pair(atype2, atype1); |
| 294 |
> |
int eamtid1 = EAMtids[ atype1->getIdent() ]; |
| 295 |
> |
int eamtid2 = EAMtids[ atype2->getIdent() ]; |
| 296 |
|
|
| 297 |
< |
MixingMap[key1] = mixer; |
| 298 |
< |
if (key2 != key1) { |
| 299 |
< |
MixingMap[key2] = mixer; |
| 297 |
> |
MixingMap[eamtid1][eamtid2] = mixer; |
| 298 |
> |
if (eamtid2 != eamtid1) { |
| 299 |
> |
MixingMap[eamtid2][eamtid1] = mixer; |
| 300 |
|
} |
| 301 |
|
return; |
| 302 |
|
} |
| 303 |
|
|
| 304 |
< |
void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, |
| 352 |
< |
RealType &rho_i_at_j, RealType &rho_j_at_i) { |
| 304 |
> |
void EAM::calcDensity(InteractionData &idat) { |
| 305 |
|
|
| 306 |
|
if (!initialized_) initialize(); |
| 307 |
|
|
| 308 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 309 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 308 |
> |
EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]]; |
| 309 |
> |
EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]]; |
| 310 |
|
|
| 311 |
< |
if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij); |
| 312 |
< |
if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij); |
| 313 |
< |
return; |
| 311 |
> |
if (haveCutoffRadius_) |
| 312 |
> |
if ( *(idat.rij) > eamRcut_) return; |
| 313 |
> |
|
| 314 |
> |
if ( *(idat.rij) < data1.rcut) { |
| 315 |
> |
if (data1.isFluctuating) { |
| 316 |
> |
*(idat.rho2) += (1.0 - *(idat.flucQ1) * data1.qToRhoScaling ) * |
| 317 |
> |
data1.rho->getValueAt( *(idat.rij) ); |
| 318 |
> |
} else { |
| 319 |
> |
*(idat.rho2) += data1.rho->getValueAt( *(idat.rij)); |
| 320 |
> |
} |
| 321 |
> |
} |
| 322 |
> |
|
| 323 |
> |
if ( *(idat.rij) < data2.rcut) { |
| 324 |
> |
if (data2.isFluctuating) { |
| 325 |
> |
*(idat.rho1) += (1.0 - *(idat.flucQ2) * data2.qToRhoScaling ) * |
| 326 |
> |
data2.rho->getValueAt( *(idat.rij) ); |
| 327 |
> |
} else { |
| 328 |
> |
*(idat.rho1) += data2.rho->getValueAt( *(idat.rij)); |
| 329 |
> |
} |
| 330 |
> |
} |
| 331 |
> |
|
| 332 |
> |
return; |
| 333 |
|
} |
| 334 |
< |
|
| 335 |
< |
void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho, |
| 336 |
< |
RealType &dfrhodrho) { |
| 366 |
< |
|
| 334 |
> |
|
| 335 |
> |
void EAM::calcFunctional(SelfData &sdat) { |
| 336 |
> |
|
| 337 |
|
if (!initialized_) initialize(); |
| 338 |
|
|
| 339 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 340 |
< |
|
| 341 |
< |
pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho); |
| 339 |
> |
EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ]; |
| 340 |
> |
|
| 341 |
> |
data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), *(sdat.dfrhodrho) ); |
| 342 |
|
|
| 343 |
< |
frho = result.first; |
| 344 |
< |
dfrhodrho = result.second; |
| 343 |
> |
(*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho); |
| 344 |
> |
if (sdat.doParticlePot) { |
| 345 |
> |
*(sdat.particlePot) += *(sdat.frho); |
| 346 |
> |
} |
| 347 |
> |
|
| 348 |
|
return; |
| 349 |
|
} |
| 350 |
|
|
| 351 |
|
|
| 352 |
< |
void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 380 |
< |
RealType rij, RealType r2, RealType sw, |
| 381 |
< |
RealType &vpair, RealType &pot, Vector3d &f1, |
| 382 |
< |
RealType rho_i, RealType rho_j, |
| 383 |
< |
RealType dfrhodrho_i, RealType dfrhodrho_j, |
| 384 |
< |
RealType &fshift_i, RealType &fshift_j) { |
| 352 |
> |
void EAM::calcForce(InteractionData &idat) { |
| 353 |
|
|
| 354 |
|
if (!initialized_) initialize(); |
| 355 |
+ |
|
| 356 |
+ |
if (haveCutoffRadius_) |
| 357 |
+ |
if ( *(idat.rij) > eamRcut_) return; |
| 358 |
+ |
|
| 359 |
+ |
|
| 360 |
+ |
int eamtid1 = EAMtids[idat.atid1]; |
| 361 |
+ |
int eamtid2 = EAMtids[idat.atid2]; |
| 362 |
|
|
| 363 |
< |
pair<RealType, RealType> res; |
| 363 |
> |
EAMAtomData &data1 = EAMdata[eamtid1]; |
| 364 |
> |
EAMAtomData &data2 = EAMdata[eamtid2]; |
| 365 |
|
|
| 366 |
< |
if (rij < eamRcut_) { |
| 367 |
< |
|
| 368 |
< |
EAMAtomData data1 = EAMMap[at1]; |
| 369 |
< |
EAMAtomData data2 = EAMMap[at2]; |
| 370 |
< |
|
| 371 |
< |
// get type-specific cutoff radii |
| 372 |
< |
|
| 373 |
< |
RealType rci = data1.rcut; |
| 374 |
< |
RealType rcj = data2.rcut; |
| 375 |
< |
|
| 376 |
< |
RealType rha, drha, rhb, drhb; |
| 377 |
< |
RealType pha, dpha, phb, dphb; |
| 378 |
< |
RealType phab, dvpdr; |
| 379 |
< |
RealType drhoidr, drhojdr, dudr; |
| 380 |
< |
|
| 381 |
< |
if (rij < rci) { |
| 406 |
< |
res = data1.rho->getValueAndDerivativeAt(rij); |
| 407 |
< |
rha = res.first; |
| 408 |
< |
drha = res.second; |
| 409 |
< |
|
| 410 |
< |
res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij); |
| 411 |
< |
pha = res.first; |
| 412 |
< |
dpha = res.second; |
| 366 |
> |
// get type-specific cutoff radii |
| 367 |
> |
|
| 368 |
> |
RealType rci = data1.rcut; |
| 369 |
> |
RealType rcj = data2.rcut; |
| 370 |
> |
|
| 371 |
> |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 372 |
> |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 373 |
> |
RealType phab(0.0), dvpdr(0.0); |
| 374 |
> |
RealType drhoidr, drhojdr, dudr; |
| 375 |
> |
|
| 376 |
> |
if ( *(idat.rij) < rci) { |
| 377 |
> |
data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha); |
| 378 |
> |
CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi; |
| 379 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha); |
| 380 |
> |
if (data1.isFluctuating) { |
| 381 |
> |
*(idat.dVdFQ1) -= *(idat.dfrho2) * rha * data1.qToRhoScaling; |
| 382 |
|
} |
| 383 |
< |
|
| 384 |
< |
if (rij < rcj) { |
| 385 |
< |
res = data2.rho->getValueAndDerivativeAt(rij); |
| 386 |
< |
rhb = res.first; |
| 387 |
< |
drhb = res.second; |
| 388 |
< |
|
| 389 |
< |
res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij); |
| 390 |
< |
phb = res.first; |
| 422 |
< |
dphb = res.second; |
| 383 |
> |
} |
| 384 |
> |
|
| 385 |
> |
if ( *(idat.rij) < rcj) { |
| 386 |
> |
data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb ); |
| 387 |
> |
CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi; |
| 388 |
> |
phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb); |
| 389 |
> |
if (data2.isFluctuating) { |
| 390 |
> |
*(idat.dVdFQ2) -= *(idat.dfrho1) * rhb * data2.qToRhoScaling; |
| 391 |
|
} |
| 392 |
+ |
} |
| 393 |
|
|
| 394 |
< |
phab = 0.0; |
| 395 |
< |
dvpdr = 0.0; |
| 396 |
< |
|
| 397 |
< |
switch(mixMeth_) { |
| 398 |
< |
case eamJohnson: |
| 399 |
< |
|
| 400 |
< |
if (rij < rci) { |
| 432 |
< |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 433 |
< |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 434 |
< |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 435 |
< |
} |
| 436 |
< |
|
| 437 |
< |
if (rij < rcj) { |
| 438 |
< |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 439 |
< |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 440 |
< |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 441 |
< |
} |
| 442 |
< |
|
| 443 |
< |
break; |
| 444 |
< |
|
| 445 |
< |
case eamDaw: |
| 446 |
< |
|
| 447 |
< |
res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij); |
| 448 |
< |
phab = res.first; |
| 449 |
< |
dvpdr = res.second; |
| 450 |
< |
|
| 451 |
< |
break; |
| 452 |
< |
case eamUnknown: |
| 453 |
< |
default: |
| 454 |
< |
|
| 455 |
< |
sprintf(painCave.errMsg, |
| 456 |
< |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 457 |
< |
); |
| 458 |
< |
painCave.severity = OPENMD_ERROR; |
| 459 |
< |
painCave.isFatal = 1; |
| 460 |
< |
simError(); |
| 461 |
< |
|
| 394 |
> |
switch(mixMeth_) { |
| 395 |
> |
case eamJohnson: |
| 396 |
> |
|
| 397 |
> |
if ( *(idat.rij) < rci) { |
| 398 |
> |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 399 |
> |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 400 |
> |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 401 |
|
} |
| 402 |
|
|
| 403 |
< |
drhoidr = drha; |
| 404 |
< |
drhojdr = drhb; |
| 403 |
> |
|
| 404 |
> |
|
| 405 |
> |
if ( *(idat.rij) < rcj) { |
| 406 |
> |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 407 |
> |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 408 |
> |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 409 |
> |
} |
| 410 |
> |
|
| 411 |
> |
break; |
| 412 |
> |
|
| 413 |
> |
case eamDaw: |
| 414 |
> |
MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr); |
| 415 |
> |
|
| 416 |
> |
break; |
| 417 |
> |
case eamUnknown: |
| 418 |
> |
default: |
| 419 |
> |
|
| 420 |
> |
sprintf(painCave.errMsg, |
| 421 |
> |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 422 |
> |
); |
| 423 |
> |
painCave.severity = OPENMD_ERROR; |
| 424 |
> |
painCave.isFatal = 1; |
| 425 |
> |
simError(); |
| 426 |
> |
|
| 427 |
> |
} |
| 428 |
> |
|
| 429 |
> |
drhoidr = drha; |
| 430 |
> |
drhojdr = drhb; |
| 431 |
> |
|
| 432 |
> |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 433 |
> |
|
| 434 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 435 |
|
|
| 467 |
– |
dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr; |
| 468 |
– |
|
| 469 |
– |
f1 = d * dudr / rij; |
| 436 |
|
|
| 437 |
< |
// particle_pot is the difference between the full potential |
| 438 |
< |
// and the full potential without the presence of a particular |
| 437 |
> |
if (idat.doParticlePot) { |
| 438 |
> |
// particlePot is the difference between the full potential and |
| 439 |
> |
// the full potential without the presence of a particular |
| 440 |
|
// particle (atom1). |
| 441 |
|
// |
| 442 |
< |
// This reduces the density at other particle locations, so |
| 443 |
< |
// we need to recompute the density at atom2 assuming atom1 |
| 444 |
< |
// didn't contribute. This then requires recomputing the |
| 445 |
< |
// density functional for atom2 as well. |
| 446 |
< |
// |
| 447 |
< |
// Most of the particle_pot heavy lifting comes from the |
| 448 |
< |
// pair interaction, and will be handled by vpair. |
| 449 |
< |
|
| 450 |
< |
fshift_i = data1.F->getValueAt( rho_i - rhb ); |
| 451 |
< |
fshift_j = data1.F->getValueAt( rho_j - rha ); |
| 485 |
< |
|
| 486 |
< |
pot += phab; |
| 487 |
< |
|
| 488 |
< |
vpair += phab; |
| 442 |
> |
// This reduces the density at other particle locations, so we |
| 443 |
> |
// need to recompute the density at atom2 assuming atom1 didn't |
| 444 |
> |
// contribute. This then requires recomputing the density |
| 445 |
> |
// functional for atom2 as well. |
| 446 |
> |
|
| 447 |
> |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 448 |
> |
- *(idat.frho2); |
| 449 |
> |
|
| 450 |
> |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 451 |
> |
- *(idat.frho1); |
| 452 |
|
} |
| 490 |
– |
|
| 491 |
– |
return; |
| 453 |
|
|
| 454 |
< |
} |
| 494 |
< |
|
| 495 |
< |
|
| 496 |
< |
void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij, |
| 497 |
< |
RealType* rho_i_at_j, RealType* rho_j_at_i){ |
| 498 |
< |
|
| 499 |
< |
if (!initialized_) initialize(); |
| 454 |
> |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 455 |
|
|
| 456 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 457 |
< |
AtomType* atype2 = EAMlist[*atid2]; |
| 456 |
> |
*(idat.vpair) += phab; |
| 457 |
> |
|
| 458 |
> |
return; |
| 459 |
|
|
| 504 |
– |
calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
| 505 |
– |
|
| 506 |
– |
return; |
| 460 |
|
} |
| 461 |
|
|
| 462 |
< |
void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho, |
| 463 |
< |
RealType *dfrhodrho) { |
| 462 |
> |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 463 |
> |
if (!initialized_) initialize(); |
| 464 |
|
|
| 465 |
< |
if (!initialized_) initialize(); |
| 465 |
> |
RealType cut = 0.0; |
| 466 |
|
|
| 467 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 468 |
< |
|
| 469 |
< |
calcFunctional(atype1, *rho, *frho, *dfrhodrho); |
| 467 |
> |
int atid1 = atypes.first->getIdent(); |
| 468 |
> |
int atid2 = atypes.second->getIdent(); |
| 469 |
> |
int eamtid1 = EAMtids[atid1]; |
| 470 |
> |
int eamtid2 = EAMtids[atid2]; |
| 471 |
|
|
| 472 |
< |
return; |
| 473 |
< |
} |
| 474 |
< |
RealType EAM::getEAMcut(int *atid1) { |
| 472 |
> |
if (eamtid1 != -1) { |
| 473 |
> |
EAMAtomData data1 = EAMdata[eamtid1]; |
| 474 |
> |
cut = data1.rcut; |
| 475 |
> |
} |
| 476 |
|
|
| 477 |
< |
if (!initialized_) initialize(); |
| 477 |
> |
if (eamtid2 != -1) { |
| 478 |
> |
EAMAtomData data2 = EAMdata[eamtid2]; |
| 479 |
> |
if (data2.rcut > cut) |
| 480 |
> |
cut = data2.rcut; |
| 481 |
> |
} |
| 482 |
|
|
| 483 |
< |
AtomType* atype1 = EAMlist[*atid1]; |
| 525 |
< |
|
| 526 |
< |
return getRcut(atype1); |
| 483 |
> |
return cut; |
| 484 |
|
} |
| 528 |
– |
|
| 529 |
– |
void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 530 |
– |
RealType *r2, RealType *sw, RealType *vpair, |
| 531 |
– |
RealType *pot, RealType *f1, RealType *rho1, |
| 532 |
– |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 533 |
– |
RealType *fshift1, RealType *fshift2) { |
| 534 |
– |
|
| 535 |
– |
if (!initialized_) initialize(); |
| 536 |
– |
|
| 537 |
– |
AtomType* atype1 = EAMlist[*atid1]; |
| 538 |
– |
AtomType* atype2 = EAMlist[*atid2]; |
| 539 |
– |
|
| 540 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 541 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 542 |
– |
|
| 543 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair, *pot, frc, |
| 544 |
– |
*rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2); |
| 545 |
– |
|
| 546 |
– |
f1[0] = frc.x(); |
| 547 |
– |
f1[1] = frc.y(); |
| 548 |
– |
f1[2] = frc.z(); |
| 549 |
– |
|
| 550 |
– |
return; |
| 551 |
– |
} |
| 552 |
– |
|
| 553 |
– |
void EAM::setCutoffEAM(RealType *thisRcut) { |
| 554 |
– |
eamRcut_ = *thisRcut; |
| 555 |
– |
} |
| 485 |
|
} |
| 486 |
|
|
| 558 |
– |
extern "C" { |
| 559 |
– |
|
| 560 |
– |
#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO) |
| 561 |
– |
#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO) |
| 562 |
– |
#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR) |
| 563 |
– |
#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM) |
| 564 |
– |
#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT) |
| 565 |
– |
|
| 566 |
– |
|
| 567 |
– |
void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, |
| 568 |
– |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 569 |
– |
|
| 570 |
– |
return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij, |
| 571 |
– |
rho_i_at_j, |
| 572 |
– |
rho_j_at_i); |
| 573 |
– |
} |
| 574 |
– |
void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, |
| 575 |
– |
RealType *dfrhodrho) { |
| 576 |
– |
|
| 577 |
– |
return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho, |
| 578 |
– |
dfrhodrho); |
| 579 |
– |
|
| 580 |
– |
} |
| 581 |
– |
void fortranSetCutoffEAM(RealType *rcut) { |
| 582 |
– |
return OpenMD::EAM::Instance()->setCutoffEAM(rcut); |
| 583 |
– |
} |
| 584 |
– |
void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 585 |
– |
RealType *r2, RealType *sw, RealType *vpair, |
| 586 |
– |
RealType *pot, RealType *f1, RealType *rho1, |
| 587 |
– |
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 588 |
– |
RealType *fshift1, RealType *fshift2){ |
| 589 |
– |
|
| 590 |
– |
return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij, |
| 591 |
– |
r2, sw, vpair, |
| 592 |
– |
pot, f1, rho1, |
| 593 |
– |
rho2, dfrho1, dfrho2, |
| 594 |
– |
fshift1, fshift2); |
| 595 |
– |
} |
| 596 |
– |
RealType fortranGetEAMcut(int* atid) { |
| 597 |
– |
return OpenMD::EAM::Instance()->getEAMcut(atid); |
| 598 |
– |
} |
| 599 |
– |
|
| 600 |
– |
} |
