| 46 |
|
#include "nonbonded/LJ.hpp" |
| 47 |
|
#include "utils/simError.h" |
| 48 |
|
|
| 49 |
– |
|
| 49 |
|
namespace OpenMD { |
| 50 |
|
|
| 51 |
< |
bool LJ::initialized_ = false; |
| 52 |
< |
bool LJ::shiftedPot_ = false; |
| 54 |
< |
bool LJ::shiftedFrc_ = false; |
| 55 |
< |
ForceField* LJ::forceField_ = NULL; |
| 56 |
< |
std::map<int, AtomType*> LJ::LJMap; |
| 57 |
< |
std::map<std::pair<AtomType*, AtomType*>, LJInteractionData> LJ::MixingMap; |
| 58 |
< |
|
| 59 |
< |
LJ* LJ::_instance = NULL; |
| 51 |
> |
LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), |
| 52 |
> |
shiftedFrc_(false), forceField_(NULL) {} |
| 53 |
|
|
| 61 |
– |
LJ* LJ::Instance() { |
| 62 |
– |
if (!_instance) { |
| 63 |
– |
_instance = new LJ(); |
| 64 |
– |
} |
| 65 |
– |
return _instance; |
| 66 |
– |
} |
| 67 |
– |
|
| 54 |
|
LJParam LJ::getLJParam(AtomType* atomType) { |
| 55 |
|
|
| 56 |
|
// Do sanity checking on the AtomType we were passed before |
| 92 |
|
return ljParam.sigma; |
| 93 |
|
} |
| 94 |
|
|
| 109 |
– |
RealType LJ::getSigma(int atid) { |
| 110 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 111 |
– |
it = LJMap.find(atid); |
| 112 |
– |
if (it == LJMap.end()) { |
| 113 |
– |
sprintf( painCave.errMsg, |
| 114 |
– |
"LJ::getSigma could not find atid %d in LJMap\n", |
| 115 |
– |
(atid)); |
| 116 |
– |
painCave.severity = OPENMD_ERROR; |
| 117 |
– |
painCave.isFatal = 1; |
| 118 |
– |
simError(); |
| 119 |
– |
} |
| 120 |
– |
AtomType* atype = it->second; |
| 121 |
– |
|
| 122 |
– |
return getSigma(atype); |
| 123 |
– |
} |
| 124 |
– |
|
| 95 |
|
RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
| 96 |
|
RealType sigma1 = getSigma(atomType1); |
| 97 |
|
RealType sigma2 = getSigma(atomType2); |
| 98 |
|
|
| 99 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 100 |
< |
std::string DistanceMix = fopts.getDistanceMixingRule(); |
| 100 |
> |
string DistanceMix = fopts.getDistanceMixingRule(); |
| 101 |
|
toUpper(DistanceMix); |
| 102 |
|
|
| 103 |
|
if (DistanceMix == "GEOMETRIC") |
| 109 |
|
RealType LJ::getEpsilon(AtomType* atomType) { |
| 110 |
|
LJParam ljParam = getLJParam(atomType); |
| 111 |
|
return ljParam.epsilon; |
| 142 |
– |
} |
| 143 |
– |
|
| 144 |
– |
RealType LJ::getEpsilon(int atid) { |
| 145 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 146 |
– |
it = LJMap.find(atid); |
| 147 |
– |
if (it == LJMap.end()) { |
| 148 |
– |
sprintf( painCave.errMsg, |
| 149 |
– |
"LJ::getEpsilon could not find atid %d in LJMap\n", |
| 150 |
– |
(atid)); |
| 151 |
– |
painCave.severity = OPENMD_ERROR; |
| 152 |
– |
painCave.isFatal = 1; |
| 153 |
– |
simError(); |
| 154 |
– |
} |
| 155 |
– |
AtomType* atype = it->second; |
| 156 |
– |
|
| 157 |
– |
return getEpsilon(atype); |
| 112 |
|
} |
| 113 |
|
|
| 114 |
|
RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
| 118 |
|
} |
| 119 |
|
|
| 120 |
|
void LJ::initialize() { |
| 121 |
< |
ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes(); |
| 121 |
> |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 122 |
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 123 |
|
AtomType* at; |
| 124 |
|
|
| 125 |
< |
for (at = atomTypes.beginType(i); at != NULL; |
| 126 |
< |
at = atomTypes.nextType(i)) { |
| 125 |
> |
for (at = atomTypes->beginType(i); at != NULL; |
| 126 |
> |
at = atomTypes->nextType(i)) { |
| 127 |
|
|
| 128 |
|
if (at->isLennardJones()) |
| 129 |
|
addType(at); |
| 130 |
|
} |
| 131 |
|
|
| 132 |
< |
ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 132 |
> |
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 133 |
|
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 134 |
|
NonBondedInteractionType* nbt; |
| 135 |
|
|
| 136 |
< |
for (nbt = nbiTypes.beginType(j); nbt != NULL; |
| 137 |
< |
nbt = nbiTypes.nextType(j)) { |
| 136 |
> |
for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 137 |
> |
nbt = nbiTypes->nextType(j)) { |
| 138 |
|
|
| 139 |
|
if (nbt->isLennardJones()) { |
| 140 |
|
|
| 141 |
< |
std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 141 |
> |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 142 |
|
|
| 143 |
|
GenericData* data = nbt->getPropertyByName("LennardJones"); |
| 144 |
|
if (data == NULL) { |
| 179 |
|
void LJ::addType(AtomType* atomType){ |
| 180 |
|
RealType sigma1 = getSigma(atomType); |
| 181 |
|
RealType epsilon1 = getEpsilon(atomType); |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
// add it to the map: |
| 184 |
|
AtomTypeProperties atp = atomType->getATP(); |
| 185 |
< |
std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
| 186 |
< |
ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
| 185 |
> |
|
| 186 |
> |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 187 |
> |
ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 188 |
|
if (ret.second == false) { |
| 189 |
|
sprintf( painCave.errMsg, |
| 190 |
|
"LJ already had a previous entry with ident %d\n", |
| 240 |
|
} |
| 241 |
|
} |
| 242 |
|
|
| 243 |
< |
void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType rij, |
| 244 |
< |
RealType r2, RealType rcut, RealType sw, RealType vdwMult, |
| 290 |
< |
RealType vpair, RealType pot, Vector3d f1) { |
| 291 |
< |
|
| 243 |
> |
void LJ::calcForce(InteractionData idat) { |
| 244 |
> |
|
| 245 |
|
if (!initialized_) initialize(); |
| 246 |
|
|
| 247 |
|
RealType ros; |
| 251 |
|
RealType myDeriv = 0.0; |
| 252 |
|
RealType myDerivC = 0.0; |
| 253 |
|
|
| 254 |
< |
std::pair<AtomType*, AtomType*> key = std::make_pair(at1, at2); |
| 254 |
> |
std::pair<AtomType*, AtomType*> key = std::make_pair(idat.atype1, |
| 255 |
> |
idat.atype2); |
| 256 |
|
LJInteractionData mixer = MixingMap[key]; |
| 257 |
|
|
| 258 |
|
RealType sigmai = mixer.sigmai; |
| 259 |
|
RealType epsilon = mixer.epsilon; |
| 260 |
|
|
| 307 |
– |
ros = rij * sigmai; |
| 261 |
|
|
| 262 |
+ |
ros = idat.rij * sigmai; |
| 263 |
+ |
|
| 264 |
|
getLJfunc(ros, myPot, myDeriv); |
| 265 |
|
|
| 266 |
|
if (shiftedPot_) { |
| 267 |
< |
rcos = rcut * sigmai; |
| 267 |
> |
rcos = idat.rcut * sigmai; |
| 268 |
|
getLJfunc(rcos, myPotC, myDerivC); |
| 269 |
|
myDerivC = 0.0; |
| 270 |
|
} else if (LJ::shiftedFrc_) { |
| 271 |
< |
rcos = rcut * sigmai; |
| 271 |
> |
rcos = idat.rcut * sigmai; |
| 272 |
|
getLJfunc(rcos, myPotC, myDerivC); |
| 273 |
< |
myPotC = myPotC + myDerivC * (rij - rcut) * sigmai; |
| 273 |
> |
myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai; |
| 274 |
|
} else { |
| 275 |
|
myPotC = 0.0; |
| 276 |
|
myDerivC = 0.0; |
| 277 |
|
} |
| 278 |
|
|
| 279 |
< |
RealType pot_temp = vdwMult * epsilon * (myPot - myPotC); |
| 280 |
< |
vpair += pot_temp; |
| 279 |
> |
RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC); |
| 280 |
> |
idat.vpair += pot_temp; |
| 281 |
|
|
| 282 |
< |
RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai; |
| 282 |
> |
RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv - |
| 283 |
> |
myDerivC)*sigmai; |
| 284 |
|
|
| 285 |
< |
pot += sw * pot_temp; |
| 286 |
< |
f1 = d * dudr / rij; |
| 285 |
> |
idat.pot += idat.sw * pot_temp; |
| 286 |
> |
idat.f1 = idat.d * dudr / idat.rij; |
| 287 |
|
|
| 288 |
|
return; |
| 333 |
– |
} |
| 289 |
|
|
| 335 |
– |
void LJ::do_lj_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 336 |
– |
RealType *r2, RealType *rcut, RealType *sw, |
| 337 |
– |
RealType *vdwMult, |
| 338 |
– |
RealType *vpair, RealType *pot, RealType *f1) { |
| 339 |
– |
|
| 340 |
– |
if (!initialized_) initialize(); |
| 341 |
– |
|
| 342 |
– |
AtomType* atype1 = LJMap[*atid1]; |
| 343 |
– |
AtomType* atype2 = LJMap[*atid2]; |
| 344 |
– |
|
| 345 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 346 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 347 |
– |
|
| 348 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, |
| 349 |
– |
*pot, frc); |
| 350 |
– |
return; |
| 290 |
|
} |
| 291 |
|
|
| 292 |
< |
void LJ::getLJfunc(const RealType r, RealType pot, RealType deriv) { |
| 292 |
> |
void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) { |
| 293 |
> |
|
| 294 |
|
RealType ri = 1.0 / r; |
| 295 |
|
RealType ri2 = ri * ri; |
| 296 |
|
RealType ri6 = ri2 * ri2 * ri2; |
| 297 |
|
RealType ri7 = ri6 * ri; |
| 298 |
|
RealType ri12 = ri6 * ri6; |
| 299 |
|
RealType ri13 = ri12 * ri; |
| 300 |
< |
|
| 300 |
> |
|
| 301 |
|
pot = 4.0 * (ri12 - ri6); |
| 302 |
|
deriv = 24.0 * (ri7 - 2.0 * ri13); |
| 303 |
+ |
|
| 304 |
|
return; |
| 305 |
|
} |
| 306 |
+ |
|
| 307 |
|
|
| 366 |
– |
|
| 367 |
– |
void LJ::setLJDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { |
| 368 |
– |
shiftedPot_ = (bool)(*sP); |
| 369 |
– |
shiftedFrc_ = (bool)(*sF); |
| 370 |
– |
} |
| 308 |
|
} |
| 372 |
– |
|
| 373 |
– |
extern "C" { |
| 374 |
– |
|
| 375 |
– |
#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA) |
| 376 |
– |
#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON) |
| 377 |
– |
#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF) |
| 378 |
– |
#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR) |
| 379 |
– |
|
| 380 |
– |
RealType fortranGetSigma(int* atid) { |
| 381 |
– |
return OpenMD::LJ::Instance()->getSigma(*atid); |
| 382 |
– |
} |
| 383 |
– |
RealType fortranGetEpsilon(int* atid) { |
| 384 |
– |
return OpenMD::LJ::Instance()->getEpsilon(*atid); |
| 385 |
– |
} |
| 386 |
– |
void fortranSetLJCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { |
| 387 |
– |
return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot, |
| 388 |
– |
shiftedFrc); |
| 389 |
– |
} |
| 390 |
– |
void fortranDoLJPair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 391 |
– |
RealType *r2, RealType *rcut, RealType *sw, |
| 392 |
– |
RealType *vdwMult, RealType* vpair, RealType* pot, |
| 393 |
– |
RealType *f1){ |
| 394 |
– |
|
| 395 |
– |
return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut, |
| 396 |
– |
sw, vdwMult, vpair, pot, f1); |
| 397 |
– |
} |
| 398 |
– |
} |
