| 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> |
| 47 |
|
#include "nonbonded/LJ.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 49 |
– |
|
| 50 |
|
namespace OpenMD { |
| 51 |
|
|
| 52 |
< |
bool LJ::initialized_ = false; |
| 53 |
< |
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; |
| 52 |
> |
LJ::LJ() : name_("LJ"), initialized_(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 |
– |
if (!initialized_) initialize(); |
| 111 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 112 |
– |
it = LJMap.find(atid); |
| 113 |
– |
if (it == LJMap.end()) { |
| 114 |
– |
sprintf( painCave.errMsg, |
| 115 |
– |
"LJ::getSigma could not find atid %d in LJMap\n", |
| 116 |
– |
(atid)); |
| 117 |
– |
painCave.severity = OPENMD_ERROR; |
| 118 |
– |
painCave.isFatal = 1; |
| 119 |
– |
simError(); |
| 120 |
– |
} |
| 121 |
– |
AtomType* atype = it->second; |
| 122 |
– |
|
| 123 |
– |
return getSigma(atype); |
| 124 |
– |
} |
| 125 |
– |
|
| 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") |
| 111 |
|
return ljParam.epsilon; |
| 112 |
|
} |
| 113 |
|
|
| 145 |
– |
RealType LJ::getEpsilon(int atid) { |
| 146 |
– |
if (!initialized_) initialize(); |
| 147 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 148 |
– |
it = LJMap.find(atid); |
| 149 |
– |
if (it == LJMap.end()) { |
| 150 |
– |
sprintf( painCave.errMsg, |
| 151 |
– |
"LJ::getEpsilon could not find atid %d in LJMap\n", |
| 152 |
– |
(atid)); |
| 153 |
– |
painCave.severity = OPENMD_ERROR; |
| 154 |
– |
painCave.isFatal = 1; |
| 155 |
– |
simError(); |
| 156 |
– |
} |
| 157 |
– |
AtomType* atype = it->second; |
| 158 |
– |
|
| 159 |
– |
return getEpsilon(atype); |
| 160 |
– |
} |
| 161 |
– |
|
| 114 |
|
RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
| 115 |
|
RealType epsilon1 = getEpsilon(atomType1); |
| 116 |
|
RealType epsilon2 = getEpsilon(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 |
|
|
| 186 |
< |
std::pair<std::map<int,AtomType*>::iterator,bool> ret; |
| 187 |
< |
ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) ); |
| 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, |
| 292 |
< |
RealType rij, RealType r2, RealType rcut, RealType sw, |
| 293 |
< |
RealType vdwMult, RealType &vpair, RealType &pot, |
| 294 |
< |
Vector3d &f1) { |
| 295 |
< |
|
| 296 |
< |
if (!initialized_) initialize(); |
| 243 |
> |
void LJ::calcForce(InteractionData &idat) { |
| 244 |
|
|
| 245 |
< |
RealType ros; |
| 299 |
< |
RealType rcos; |
| 300 |
< |
RealType myPot = 0.0; |
| 301 |
< |
RealType myPotC = 0.0; |
| 302 |
< |
RealType myDeriv = 0.0; |
| 303 |
< |
RealType myDerivC = 0.0; |
| 245 |
> |
if (!initialized_) initialize(); |
| 246 |
|
|
| 247 |
< |
std::pair<AtomType*, AtomType*> key = std::make_pair(at1, at2); |
| 248 |
< |
LJInteractionData mixer = MixingMap[key]; |
| 307 |
< |
|
| 308 |
< |
RealType sigmai = mixer.sigmai; |
| 309 |
< |
RealType epsilon = mixer.epsilon; |
| 247 |
> |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 248 |
> |
it = MixingMap.find( idat.atypes ); |
| 249 |
|
|
| 250 |
< |
|
| 251 |
< |
ros = rij * sigmai; |
| 252 |
< |
|
| 253 |
< |
getLJfunc(ros, myPot, myDeriv); |
| 250 |
> |
if (it != MixingMap.end()) { |
| 251 |
> |
|
| 252 |
> |
LJInteractionData mixer = (*it).second; |
| 253 |
> |
|
| 254 |
> |
RealType sigmai = mixer.sigmai; |
| 255 |
> |
RealType epsilon = mixer.epsilon; |
| 256 |
> |
|
| 257 |
> |
RealType ros; |
| 258 |
> |
RealType rcos; |
| 259 |
> |
RealType myPot = 0.0; |
| 260 |
> |
RealType myPotC = 0.0; |
| 261 |
> |
RealType myDeriv = 0.0; |
| 262 |
> |
RealType myDerivC = 0.0; |
| 263 |
> |
|
| 264 |
> |
ros = *(idat.rij) * sigmai; |
| 265 |
> |
|
| 266 |
> |
getLJfunc(ros, myPot, myDeriv); |
| 267 |
> |
|
| 268 |
> |
if (idat.shiftedPot) { |
| 269 |
> |
rcos = *(idat.rcut) * sigmai; |
| 270 |
> |
getLJfunc(rcos, myPotC, myDerivC); |
| 271 |
> |
myDerivC = 0.0; |
| 272 |
> |
} else if (idat.shiftedForce) { |
| 273 |
> |
rcos = *(idat.rcut) * sigmai; |
| 274 |
> |
getLJfunc(rcos, myPotC, myDerivC); |
| 275 |
> |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
| 276 |
> |
} else { |
| 277 |
> |
myPotC = 0.0; |
| 278 |
> |
myDerivC = 0.0; |
| 279 |
> |
} |
| 280 |
|
|
| 281 |
< |
if (shiftedPot_) { |
| 282 |
< |
rcos = rcut * sigmai; |
| 283 |
< |
getLJfunc(rcos, myPotC, myDerivC); |
| 284 |
< |
myDerivC = 0.0; |
| 285 |
< |
} else if (LJ::shiftedFrc_) { |
| 321 |
< |
rcos = rcut * sigmai; |
| 322 |
< |
getLJfunc(rcos, myPotC, myDerivC); |
| 323 |
< |
myPotC = myPotC + myDerivC * (rij - rcut) * sigmai; |
| 324 |
< |
} else { |
| 325 |
< |
myPotC = 0.0; |
| 326 |
< |
myDerivC = 0.0; |
| 327 |
< |
} |
| 281 |
> |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 282 |
> |
*(idat.vpair) += pot_temp; |
| 283 |
> |
|
| 284 |
> |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 285 |
> |
myDerivC)*sigmai; |
| 286 |
|
|
| 287 |
< |
RealType pot_temp = vdwMult * epsilon * (myPot - myPotC); |
| 288 |
< |
vpair += pot_temp; |
| 289 |
< |
|
| 332 |
< |
RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai; |
| 333 |
< |
|
| 334 |
< |
pot += sw * pot_temp; |
| 335 |
< |
f1 = d * dudr / rij; |
| 336 |
< |
|
| 287 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 288 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 289 |
> |
} |
| 290 |
|
return; |
| 338 |
– |
|
| 339 |
– |
|
| 340 |
– |
|
| 291 |
|
} |
| 342 |
– |
|
| 343 |
– |
void LJ::do_lj_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 344 |
– |
RealType *r2, RealType *rcut, RealType *sw, |
| 345 |
– |
RealType *vdwMult, |
| 346 |
– |
RealType *vpair, RealType *pot, RealType *f1) { |
| 347 |
– |
|
| 348 |
– |
if (!initialized_) initialize(); |
| 349 |
– |
|
| 350 |
– |
AtomType* atype1 = LJMap[*atid1]; |
| 351 |
– |
AtomType* atype2 = LJMap[*atid2]; |
| 352 |
– |
|
| 353 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 354 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 355 |
– |
|
| 356 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, |
| 357 |
– |
*pot, frc); |
| 358 |
– |
|
| 359 |
– |
f1[0] = frc.x(); |
| 360 |
– |
f1[1] = frc.y(); |
| 361 |
– |
f1[2] = frc.z(); |
| 362 |
– |
|
| 363 |
– |
return; |
| 364 |
– |
} |
| 292 |
|
|
| 293 |
|
void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) { |
| 294 |
|
|
| 305 |
|
return; |
| 306 |
|
} |
| 307 |
|
|
| 308 |
< |
|
| 309 |
< |
void LJ::setLJDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { |
| 310 |
< |
shiftedPot_ = (bool)(*sP); |
| 311 |
< |
shiftedFrc_ = (bool)(*sF); |
| 308 |
> |
RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 309 |
> |
if (!initialized_) initialize(); |
| 310 |
> |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 311 |
> |
it = MixingMap.find(atypes); |
| 312 |
> |
if (it == MixingMap.end()) |
| 313 |
> |
return 0.0; |
| 314 |
> |
else { |
| 315 |
> |
LJInteractionData mixer = (*it).second; |
| 316 |
> |
return 2.5 * mixer.sigma; |
| 317 |
> |
} |
| 318 |
|
} |
| 386 |
– |
} |
| 319 |
|
|
| 388 |
– |
extern "C" { |
| 389 |
– |
|
| 390 |
– |
#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA) |
| 391 |
– |
#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON) |
| 392 |
– |
#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF) |
| 393 |
– |
#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR) |
| 394 |
– |
|
| 395 |
– |
RealType fortranGetSigma(int* atid) { |
| 396 |
– |
return OpenMD::LJ::Instance()->getSigma(*atid); |
| 397 |
– |
} |
| 398 |
– |
RealType fortranGetEpsilon(int* atid) { |
| 399 |
– |
return OpenMD::LJ::Instance()->getEpsilon(*atid); |
| 400 |
– |
} |
| 401 |
– |
void fortranSetLJCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { |
| 402 |
– |
return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot, |
| 403 |
– |
shiftedFrc); |
| 404 |
– |
} |
| 405 |
– |
void fortranDoLJPair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 406 |
– |
RealType *r2, RealType *rcut, RealType *sw, |
| 407 |
– |
RealType *vdwMult, RealType* vpair, RealType* pot, |
| 408 |
– |
RealType *f1){ |
| 409 |
– |
|
| 410 |
– |
return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut, |
| 411 |
– |
sw, vdwMult, vpair, pot, f1); |
| 412 |
– |
} |
| 320 |
|
} |
