| 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> |
| 46 |
|
#include <cmath> |
| 47 |
|
#include "nonbonded/LJ.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
+ |
#include "types/LennardJonesInteractionType.hpp" |
| 50 |
|
|
| 51 |
|
namespace OpenMD { |
| 52 |
|
|
| 53 |
< |
LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), |
| 52 |
< |
shiftedFrc_(false), forceField_(NULL) {} |
| 53 |
> |
LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} |
| 54 |
|
|
| 55 |
|
LJParam LJ::getLJParam(AtomType* atomType) { |
| 56 |
|
|
| 125 |
|
|
| 126 |
|
for (at = atomTypes->beginType(i); at != NULL; |
| 127 |
|
at = atomTypes->nextType(i)) { |
| 128 |
< |
|
| 129 |
< |
if (at->isLennardJones()) |
| 130 |
< |
addType(at); |
| 128 |
> |
if (at->isLennardJones()){ |
| 129 |
> |
addType(at); |
| 130 |
> |
} |
| 131 |
|
} |
| 131 |
– |
|
| 132 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 133 |
|
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 134 |
|
NonBondedInteractionType* nbt; |
| 135 |
+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
| 136 |
|
|
| 137 |
+ |
|
| 138 |
|
for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 139 |
|
nbt = nbiTypes->nextType(j)) { |
| 140 |
< |
|
| 140 |
> |
|
| 141 |
|
if (nbt->isLennardJones()) { |
| 142 |
< |
|
| 143 |
< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 144 |
< |
|
| 145 |
< |
GenericData* data = nbt->getPropertyByName("LennardJones"); |
| 146 |
< |
if (data == NULL) { |
| 147 |
< |
sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n" |
| 148 |
< |
"\tLennard-Jones parameters for %s - %s interaction.\n", |
| 147 |
< |
atypes.first->getName().c_str(), |
| 148 |
< |
atypes.second->getName().c_str()); |
| 149 |
< |
painCave.severity = OPENMD_ERROR; |
| 150 |
< |
painCave.isFatal = 1; |
| 151 |
< |
simError(); |
| 152 |
< |
} |
| 153 |
< |
|
| 154 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 155 |
< |
if (ljData == NULL) { |
| 142 |
> |
keys = nbiTypes->getKeys(j); |
| 143 |
> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
| 144 |
> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
| 145 |
> |
|
| 146 |
> |
LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt); |
| 147 |
> |
|
| 148 |
> |
if (ljit == NULL) { |
| 149 |
|
sprintf( painCave.errMsg, |
| 150 |
< |
"LJ::rebuildMixingMap could not convert GenericData to\n" |
| 151 |
< |
"\tLJParam for %s - %s interaction.\n", |
| 152 |
< |
atypes.first->getName().c_str(), |
| 153 |
< |
atypes.second->getName().c_str()); |
| 150 |
> |
"LJ::initialize could not convert NonBondedInteractionType\n" |
| 151 |
> |
"\tto LennardJonesInteractionType for %s - %s interaction.\n", |
| 152 |
> |
at1->getName().c_str(), |
| 153 |
> |
at2->getName().c_str()); |
| 154 |
|
painCave.severity = OPENMD_ERROR; |
| 155 |
|
painCave.isFatal = 1; |
| 156 |
|
simError(); |
| 157 |
|
} |
| 165 |
– |
|
| 166 |
– |
LJParam ljParam = ljData->getData(); |
| 158 |
|
|
| 159 |
< |
RealType sigma = ljParam.sigma; |
| 160 |
< |
RealType epsilon = ljParam.epsilon; |
| 161 |
< |
|
| 171 |
< |
addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon); |
| 159 |
> |
RealType sigma = ljit->getSigma(); |
| 160 |
> |
RealType epsilon = ljit->getEpsilon(); |
| 161 |
> |
addExplicitInteraction(at1, at2, sigma, epsilon); |
| 162 |
|
} |
| 163 |
|
} |
| 164 |
|
initialized_ = true; |
| 210 |
|
|
| 211 |
|
void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){ |
| 212 |
|
|
| 223 |
– |
// in case these weren't already in the map |
| 224 |
– |
addType(atype1); |
| 225 |
– |
addType(atype2); |
| 226 |
– |
|
| 213 |
|
LJInteractionData mixer; |
| 214 |
|
mixer.sigma = sigma; |
| 215 |
|
mixer.epsilon = epsilon; |
| 226 |
|
} |
| 227 |
|
} |
| 228 |
|
|
| 229 |
< |
void LJ::calcForce(InteractionData idat) { |
| 244 |
< |
|
| 229 |
> |
void LJ::calcForce(InteractionData &idat) { |
| 230 |
|
if (!initialized_) initialize(); |
| 246 |
– |
|
| 247 |
– |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 231 |
|
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 232 |
< |
it = MixingMap.find(key); |
| 232 |
> |
it = MixingMap.find( idat.atypes ); |
| 233 |
|
|
| 234 |
|
if (it != MixingMap.end()) { |
| 235 |
|
|
| 245 |
|
RealType myDeriv = 0.0; |
| 246 |
|
RealType myDerivC = 0.0; |
| 247 |
|
|
| 248 |
< |
ros = idat.rij * sigmai; |
| 248 |
> |
ros = *(idat.rij) * sigmai; |
| 249 |
|
|
| 250 |
|
getLJfunc(ros, myPot, myDeriv); |
| 251 |
|
|
| 252 |
< |
if (shiftedPot_) { |
| 253 |
< |
rcos = idat.rcut * sigmai; |
| 252 |
> |
if (idat.shiftedPot) { |
| 253 |
> |
rcos = *(idat.rcut) * sigmai; |
| 254 |
|
getLJfunc(rcos, myPotC, myDerivC); |
| 255 |
|
myDerivC = 0.0; |
| 256 |
< |
} else if (LJ::shiftedFrc_) { |
| 257 |
< |
rcos = idat.rcut * sigmai; |
| 256 |
> |
} else if (idat.shiftedForce) { |
| 257 |
> |
rcos = *(idat.rcut) * sigmai; |
| 258 |
|
getLJfunc(rcos, myPotC, myDerivC); |
| 259 |
< |
myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai; |
| 259 |
> |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
| 260 |
|
} else { |
| 261 |
|
myPotC = 0.0; |
| 262 |
|
myDerivC = 0.0; |
| 263 |
|
} |
| 264 |
|
|
| 265 |
< |
RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC); |
| 266 |
< |
idat.vpair += pot_temp; |
| 265 |
> |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 266 |
> |
*(idat.vpair) += pot_temp; |
| 267 |
|
|
| 268 |
< |
RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv - |
| 269 |
< |
myDerivC)*sigmai; |
| 270 |
< |
|
| 271 |
< |
idat.pot += idat.sw * pot_temp; |
| 272 |
< |
idat.f1 = idat.d * dudr / idat.rij; |
| 290 |
< |
|
| 268 |
> |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 269 |
> |
myDerivC)*sigmai; |
| 270 |
> |
|
| 271 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 272 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 273 |
|
} |
| 274 |
|
return; |
| 275 |
|
} |
| 289 |
|
return; |
| 290 |
|
} |
| 291 |
|
|
| 292 |
< |
RealType LJ::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 292 |
> |
RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 293 |
|
if (!initialized_) initialize(); |
| 312 |
– |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 294 |
|
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 295 |
< |
it = MixingMap.find(key); |
| 295 |
> |
it = MixingMap.find(atypes); |
| 296 |
|
if (it == MixingMap.end()) |
| 297 |
|
return 0.0; |
| 298 |
|
else { |
