| 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). |
| 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 |
|
*/ |
| 88 |
|
*/ |
| 89 |
|
|
| 90 |
|
|
| 91 |
< |
GB::GB() : name_("GB"), initialized_(false), mu_(2.0), nu_(1.0), forceField_(NULL) {} |
| 91 |
> |
GB::GB() : initialized_(false), name_("GB"), forceField_(NULL), |
| 92 |
> |
mu_(2.0), nu_(1.0) {} |
| 93 |
|
|
| 94 |
|
void GB::initialize() { |
| 95 |
|
|
| 96 |
+ |
GBtypes.clear(); |
| 97 |
+ |
GBtids.clear(); |
| 98 |
+ |
MixingMap.clear(); |
| 99 |
+ |
nGB_ = 0; |
| 100 |
+ |
|
| 101 |
+ |
GBtids.resize( forceField_->getNAtomType(), -1); |
| 102 |
+ |
|
| 103 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 104 |
|
mu_ = fopts.getGayBerneMu(); |
| 105 |
|
nu_ = fopts.getGayBerneNu(); |
| 98 |
– |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 99 |
– |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 100 |
– |
AtomType* at; |
| 106 |
|
|
| 107 |
|
// GB handles all of the GB-GB interactions as well as GB-LJ cross |
| 108 |
|
// interactions: |
| 109 |
+ |
set<AtomType*>::iterator at; |
| 110 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 111 |
+ |
if ((*at)->isGayBerne()) nGB_++; |
| 112 |
+ |
if ((*at)->isLennardJones()) nGB_++; |
| 113 |
+ |
} |
| 114 |
|
|
| 115 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 116 |
< |
at = atomTypes->nextType(i)) { |
| 117 |
< |
|
| 108 |
< |
LennardJonesAdapter lja = LennardJonesAdapter(at); |
| 109 |
< |
GayBerneAdapter gba = GayBerneAdapter(at); |
| 110 |
< |
|
| 111 |
< |
if (gba.isGayBerne() || lja.isLennardJones()) |
| 112 |
< |
addType(at); |
| 115 |
> |
MixingMap.resize(nGB_); |
| 116 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 117 |
> |
if ((*at)->isGayBerne() || (*at)->isLennardJones()) addType( *at ); |
| 118 |
|
} |
| 119 |
< |
|
| 119 |
> |
|
| 120 |
|
initialized_ = true; |
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
void GB::addType(AtomType* atomType){ |
| 119 |
– |
// add it to the map: |
| 124 |
|
|
| 125 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 126 |
< |
ret = GBMap.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
| 125 |
> |
// add it to the map: |
| 126 |
> |
int atid = atomType->getIdent(); |
| 127 |
> |
int gbtid = GBtypes.size(); |
| 128 |
> |
|
| 129 |
> |
pair<set<int>::iterator,bool> ret; |
| 130 |
> |
ret = GBtypes.insert( atid ); |
| 131 |
|
if (ret.second == false) { |
| 132 |
|
sprintf( painCave.errMsg, |
| 133 |
|
"GB already had a previous entry with ident %d\n", |
| 134 |
< |
atomType->getIdent() ); |
| 134 |
> |
atid) ; |
| 135 |
|
painCave.severity = OPENMD_INFO; |
| 136 |
|
painCave.isFatal = 0; |
| 137 |
|
simError(); |
| 138 |
|
} |
| 139 |
+ |
|
| 140 |
+ |
GBtids[atid] = gbtid; |
| 141 |
+ |
MixingMap[gbtid].resize( nGB_ ); |
| 142 |
|
|
| 143 |
< |
RealType d1, l1, eX1, eS1, eE1, dw1; |
| 144 |
< |
|
| 143 |
> |
RealType d1(0.0), l1(0.0), eX1(0.0), eS1(0.0), eE1(0.0), dw1(0.0); |
| 144 |
> |
|
| 145 |
|
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
| 146 |
|
GayBerneAdapter gba1 = GayBerneAdapter(atomType); |
| 147 |
|
if (gba1.isGayBerne()) { |
| 168 |
|
simError(); |
| 169 |
|
} |
| 170 |
|
|
| 171 |
< |
|
| 171 |
> |
|
| 172 |
|
// Now, iterate over all known types and add to the mixing map: |
| 173 |
|
|
| 174 |
< |
map<int, AtomType*>::iterator it; |
| 175 |
< |
for( it = GBMap.begin(); it != GBMap.end(); ++it) { |
| 174 |
> |
std::set<int>::iterator it; |
| 175 |
> |
for( it = GBtypes.begin(); it != GBtypes.end(); ++it) { |
| 176 |
|
|
| 177 |
< |
AtomType* atype2 = (*it).second; |
| 177 |
> |
int gbtid2 = GBtids[ (*it) ]; |
| 178 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 179 |
> |
|
| 180 |
|
LennardJonesAdapter lja2 = LennardJonesAdapter(atype2); |
| 181 |
|
GayBerneAdapter gba2 = GayBerneAdapter(atype2); |
| 182 |
< |
RealType d2, l2, eX2, eS2, eE2, dw2; |
| 182 |
> |
RealType d2(0.0), l2(0.0), eX2(0.0), eS2(0.0), eE2(0.0), dw2(0.0); |
| 183 |
|
|
| 184 |
|
if (gba2.isGayBerne()) { |
| 185 |
|
d2 = gba2.getD(); |
| 195 |
|
eS2 = eX2; |
| 196 |
|
eE2 = eX2; |
| 197 |
|
dw2 = 1.0; |
| 198 |
< |
} |
| 199 |
< |
|
| 198 |
> |
} else { |
| 199 |
> |
sprintf( painCave.errMsg, |
| 200 |
> |
"GB::addType found an atomType (%s) that does not\n" |
| 201 |
> |
"\tappear to be a Gay-Berne or Lennard-Jones atom.\n", |
| 202 |
> |
atype2->getName().c_str()); |
| 203 |
> |
painCave.severity = OPENMD_ERROR; |
| 204 |
> |
painCave.isFatal = 1; |
| 205 |
> |
simError(); |
| 206 |
> |
} |
| 207 |
> |
|
| 208 |
> |
|
| 209 |
|
GBInteractionData mixer1, mixer2; |
| 210 |
|
|
| 211 |
|
// Cleaver paper uses sqrt of squares to get sigma0 for |
| 212 |
|
// mixed interactions. |
| 213 |
< |
|
| 213 |
> |
|
| 214 |
|
mixer1.sigma0 = sqrt(d1*d1 + d2*d2); |
| 215 |
|
mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
| 216 |
|
mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
| 217 |
|
mixer1.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
| 218 |
|
((l2*l2 + d1*d1) * (l1*l1 + d2*d2)); |
| 219 |
< |
|
| 219 |
> |
|
| 220 |
|
mixer2.sigma0 = mixer1.sigma0; |
| 221 |
|
// xa2 and xai2 for j-i pairs are reversed from the same i-j pairing. |
| 222 |
|
// Swapping the particles reverses the anisotropy parameters: |
| 223 |
|
mixer2.xa2 = mixer1.xai2; |
| 224 |
|
mixer2.xai2 = mixer1.xa2; |
| 225 |
|
mixer2.x2 = mixer1.x2; |
| 226 |
< |
|
| 226 |
> |
|
| 227 |
|
// assumed LB mixing rules for now: |
| 228 |
< |
|
| 228 |
> |
|
| 229 |
|
mixer1.dw = 0.5 * (dw1 + dw2); |
| 230 |
|
mixer1.eps0 = sqrt(eX1 * eX2); |
| 231 |
|
|
| 232 |
|
mixer2.dw = mixer1.dw; |
| 233 |
|
mixer2.eps0 = mixer1.eps0; |
| 234 |
< |
|
| 234 |
> |
|
| 235 |
|
RealType mi = RealType(1.0)/mu_; |
| 236 |
|
|
| 237 |
|
mixer1.xpap2 = (pow(eS1, mi) - pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)); |
| 238 |
|
mixer1.xpapi2 = (pow(eS2, mi) - pow(eE2, mi)) / (pow(eS2, mi) + pow(eE1, mi)); |
| 239 |
|
mixer1.xp2 = (pow(eS1, mi) - pow(eE1, mi)) * (pow(eS2, mi) - pow(eE2, mi)) / |
| 240 |
|
(pow(eS2, mi) + pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)) ; |
| 241 |
< |
|
| 241 |
> |
|
| 242 |
|
// xpap2 and xpapi2 for j-i pairs are reversed from the same i-j pairing. |
| 243 |
|
// Swapping the particles reverses the anisotropy parameters: |
| 244 |
|
mixer2.xpap2 = mixer1.xpapi2; |
| 245 |
|
mixer2.xpapi2 = mixer1.xpap2; |
| 246 |
|
mixer2.xp2 = mixer1.xp2; |
| 247 |
+ |
// keep track of who is the LJ atom: |
| 248 |
+ |
mixer1.i_is_LJ = atomType->isLennardJones(); |
| 249 |
+ |
mixer1.j_is_LJ = atype2->isLennardJones(); |
| 250 |
+ |
mixer2.i_is_LJ = mixer1.j_is_LJ; |
| 251 |
+ |
mixer2.j_is_LJ = mixer1.i_is_LJ; |
| 252 |
|
|
| 253 |
+ |
|
| 254 |
|
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 255 |
|
|
| 256 |
|
if (gba1.isGayBerne() || gba2.isGayBerne()) { |
| 257 |
< |
|
| 258 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 259 |
< |
key1 = make_pair(atomType, atype2); |
| 260 |
< |
key2 = make_pair(atype2, atomType); |
| 261 |
< |
|
| 234 |
< |
MixingMap[key1] = mixer1; |
| 235 |
< |
if (key2 != key1) { |
| 236 |
< |
MixingMap[key2] = mixer2; |
| 237 |
< |
} |
| 257 |
> |
MixingMap[gbtid2].resize( nGB_ ); |
| 258 |
> |
MixingMap[gbtid][gbtid2] = mixer1; |
| 259 |
> |
if (gbtid2 != gbtid) { |
| 260 |
> |
MixingMap[gbtid2][gbtid] = mixer2; |
| 261 |
> |
} |
| 262 |
|
} |
| 263 |
< |
} |
| 263 |
> |
} |
| 264 |
|
} |
| 265 |
|
|
| 266 |
|
void GB::calcForce(InteractionData &idat) { |
| 267 |
|
|
| 268 |
|
if (!initialized_) initialize(); |
| 269 |
|
|
| 270 |
< |
GBInteractionData mixer = MixingMap[idat.atypes]; |
| 270 |
> |
GBInteractionData &mixer = MixingMap[GBtids[idat.atid1]][GBtids[idat.atid2]]; |
| 271 |
|
|
| 272 |
|
RealType sigma0 = mixer.sigma0; |
| 273 |
|
RealType dw = mixer.dw; |
| 279 |
|
RealType xpap2 = mixer.xpap2; |
| 280 |
|
RealType xpapi2 = mixer.xpapi2; |
| 281 |
|
|
| 258 |
– |
// cerr << "atypes = " << idat.atypes.first->getName() << " " << idat.atypes.second->getName() << "\n"; |
| 259 |
– |
// cerr << "sigma0 = " <<mixer.sigma0 <<"\n"; |
| 260 |
– |
// cerr << "dw = " <<mixer.dw <<"\n"; |
| 261 |
– |
// cerr << "eps0 = " <<mixer.eps0 <<"\n"; |
| 262 |
– |
// cerr << "x2 = " <<mixer.x2 <<"\n"; |
| 263 |
– |
// cerr << "xa2 = " <<mixer.xa2 <<"\n"; |
| 264 |
– |
// cerr << "xai2 = " <<mixer.xai2 <<"\n"; |
| 265 |
– |
// cerr << "xp2 = " <<mixer.xp2 <<"\n"; |
| 266 |
– |
// cerr << "xpap2 = " <<mixer.xpap2 <<"\n"; |
| 267 |
– |
// cerr << "xpapi2 = " <<mixer.xpapi2 <<"\n"; |
| 268 |
– |
|
| 282 |
|
Vector3d ul1 = idat.A1->getRow(2); |
| 283 |
|
Vector3d ul2 = idat.A2->getRow(2); |
| 284 |
|
|
| 272 |
– |
// cerr << "ul1 = " <<ul1<<"\n"; |
| 273 |
– |
// cerr << "ul2 = " <<ul2<<"\n"; |
| 274 |
– |
|
| 285 |
|
RealType a, b, g; |
| 276 |
– |
|
| 277 |
– |
// This is not good. We should store this in the mixing map, and not |
| 278 |
– |
// query atom types in calc force. |
| 279 |
– |
bool i_is_LJ = idat.atypes.first->isLennardJones(); |
| 280 |
– |
bool j_is_LJ = idat.atypes.second->isLennardJones(); |
| 286 |
|
|
| 287 |
< |
if (i_is_LJ) { |
| 287 |
> |
if (mixer.i_is_LJ) { |
| 288 |
|
a = 0.0; |
| 289 |
|
ul1 = V3Zero; |
| 290 |
|
} else { |
| 291 |
|
a = dot(*(idat.d), ul1); |
| 292 |
|
} |
| 293 |
|
|
| 294 |
< |
if (j_is_LJ) { |
| 294 |
> |
if (mixer.j_is_LJ) { |
| 295 |
|
b = 0.0; |
| 296 |
|
ul2 = V3Zero; |
| 297 |
|
} else { |
| 298 |
|
b = dot(*(idat.d), ul2); |
| 299 |
|
} |
| 300 |
|
|
| 301 |
< |
if (i_is_LJ || j_is_LJ) |
| 301 |
> |
if (mixer.i_is_LJ || mixer.j_is_LJ) |
| 302 |
|
g = 0.0; |
| 303 |
|
else |
| 304 |
|
g = dot(ul1, ul2); |
| 313 |
|
RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
| 314 |
|
RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
| 315 |
|
|
| 311 |
– |
// cerr << "au2 = " << au2 << "\n"; |
| 312 |
– |
// cerr << "bu2 = " << bu2 << "\n"; |
| 313 |
– |
// cerr << "g2 = " << g2 << "\n"; |
| 314 |
– |
// cerr << "H = " << H << "\n"; |
| 315 |
– |
// cerr << "Hp = " << Hp << "\n"; |
| 316 |
– |
|
| 316 |
|
RealType sigma = sigma0 / sqrt(1.0 - H); |
| 317 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 318 |
|
RealType e2 = 1.0 - Hp; |
| 330 |
|
RealType s3 = sigma*sigma*sigma; |
| 331 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 332 |
|
|
| 334 |
– |
// cerr << "vdwMult = " << *(idat.vdwMult) << "\n"; |
| 335 |
– |
// cerr << "eps = " << eps <<"\n"; |
| 336 |
– |
// cerr << "mu = " << mu_ << "\n"; |
| 337 |
– |
// cerr << "R12 = " << R12 << "\n"; |
| 338 |
– |
// cerr << "R6 = " << R6 << "\n"; |
| 339 |
– |
// cerr << "R13 = " << R13 << "\n"; |
| 340 |
– |
// cerr << "R7 = " << R7 << "\n"; |
| 341 |
– |
// cerr << "e2 = " << e2 << "\n"; |
| 342 |
– |
// cerr << "rij = " << *(idat.rij) << "\n"; |
| 343 |
– |
// cerr << "s3 = " << s3 << "\n"; |
| 344 |
– |
// cerr << "s03 = " << s03 << "\n"; |
| 345 |
– |
// cerr << "dw = " << dw << "\n"; |
| 346 |
– |
|
| 333 |
|
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 334 |
|
(e2 * *(idat.rij)); |
| 335 |
|
|
| 344 |
|
|
| 345 |
|
RealType dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0 - xp2 * g2) |
| 346 |
|
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0 - x2 * g2); |
| 347 |
< |
|
| 347 |
> |
|
| 348 |
|
RealType dUdg = 4.0 * eps * nu_ * (R12 - R6) * x2 * g / (1.0 - x2*g2) |
| 349 |
|
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 350 |
|
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 351 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 352 |
< |
|
| 367 |
< |
// cerr << "pref = " << pref1 << " " << pref2 << "\n"; |
| 368 |
< |
// cerr << "dU = " << dUdr << " " << dUda <<" " << dUdb << " " << dUdg << "\n"; |
| 369 |
< |
|
| 352 |
> |
|
| 353 |
|
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 354 |
|
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 355 |
|
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 356 |
|
Vector3d uxu = cross(ul1, ul2); |
| 357 |
< |
|
| 357 |
> |
|
| 358 |
|
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 359 |
|
*(idat.f1) += (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw); |
| 360 |
|
*(idat.t1) += (dUda * rxu1 - dUdg * uxu) * *(idat.sw); |
| 361 |
|
*(idat.t2) += (dUdb * rxu2 + dUdg * uxu) * *(idat.sw); |
| 362 |
|
*(idat.vpair) += U; |
| 363 |
|
|
| 381 |
– |
// cerr << "f1 term = " << (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw) << "\n"; |
| 382 |
– |
// cerr << "t1 term = " << (dUda * rxu1 - dUdg * uxu) * *(idat.sw) << "\n"; |
| 383 |
– |
// cerr << "t2 term = " << (dUdb * rxu2 + dUdg * uxu) * *(idat.sw) << "\n"; |
| 384 |
– |
// cerr << "vp term = " << U << "\n"; |
| 385 |
– |
|
| 364 |
|
return; |
| 365 |
|
|
| 366 |
|
} |
