| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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< |
* [4] Vardeman & Gezelter, in progress (2009). |
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> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <stdio.h> |
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namespace OpenMD { |
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|
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< |
LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), |
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< |
shiftedFrc_(false), forceField_(NULL) {} |
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> |
LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} |
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|
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LJParam LJ::getLJParam(AtomType* atomType) { |
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|
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} |
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} |
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< |
void LJ::calcForce(InteractionData idat) { |
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> |
void LJ::calcForce(InteractionData &idat) { |
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if (!initialized_) initialize(); |
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< |
|
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< |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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> |
|
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map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
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< |
it = MixingMap.find(key); |
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> |
it = MixingMap.find( idat.atypes ); |
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|
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if (it != MixingMap.end()) { |
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RealType myDeriv = 0.0; |
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RealType myDerivC = 0.0; |
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|
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< |
ros = idat.rij * sigmai; |
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> |
ros = *(idat.rij) * sigmai; |
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getLJfunc(ros, myPot, myDeriv); |
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< |
if (shiftedPot_) { |
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< |
rcos = idat.rcut * sigmai; |
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> |
if (idat.shiftedPot) { |
| 269 |
> |
rcos = *(idat.rcut) * sigmai; |
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getLJfunc(rcos, myPotC, myDerivC); |
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myDerivC = 0.0; |
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< |
} else if (LJ::shiftedFrc_) { |
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< |
rcos = idat.rcut * sigmai; |
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> |
} else if (idat.shiftedForce) { |
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> |
rcos = *(idat.rcut) * sigmai; |
| 274 |
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getLJfunc(rcos, myPotC, myDerivC); |
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< |
myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai; |
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> |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
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} else { |
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myPotC = 0.0; |
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myDerivC = 0.0; |
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} |
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|
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< |
RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC); |
| 282 |
< |
idat.vpair += pot_temp; |
| 281 |
> |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 282 |
> |
*(idat.vpair) += pot_temp; |
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|
| 284 |
< |
RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv - |
| 285 |
< |
myDerivC)*sigmai; |
| 286 |
< |
|
| 287 |
< |
idat.pot += idat.sw * pot_temp; |
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< |
idat.f1 = idat.d * dudr / idat.rij; |
| 290 |
< |
|
| 284 |
> |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 285 |
> |
myDerivC)*sigmai; |
| 286 |
> |
|
| 287 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 288 |
> |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 289 |
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} |
| 290 |
|
return; |
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} |
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return; |
| 306 |
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} |
| 307 |
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|
| 308 |
< |
RealType LJ::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 308 |
> |
RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 309 |
|
if (!initialized_) initialize(); |
| 312 |
– |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 310 |
|
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 311 |
< |
it = MixingMap.find(key); |
| 311 |
> |
it = MixingMap.find(atypes); |
| 312 |
|
if (it == MixingMap.end()) |
| 313 |
|
return 0.0; |
| 314 |
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else { |
