| 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 |
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|
| 43 |
|
#include <stdio.h> |
| 51 |
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|
| 52 |
|
namespace OpenMD { |
| 53 |
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|
| 54 |
< |
MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL), |
| 54 |
< |
shiftedPot_(false), shiftedFrc_(false) {} |
| 54 |
> |
MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL) {} |
| 55 |
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|
| 56 |
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void MAW::initialize() { |
| 57 |
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|
| 58 |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 59 |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 60 |
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NonBondedInteractionType* nbt; |
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+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
| 62 |
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|
| 63 |
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 64 |
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nbt = nbiTypes->nextType(j)) { |
| 65 |
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|
| 66 |
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if (nbt->isMAW()) { |
| 67 |
< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 68 |
< |
|
| 69 |
< |
GenericData* data = nbt->getPropertyByName("MAW"); |
| 70 |
< |
if (data == NULL) { |
| 71 |
< |
sprintf( painCave.errMsg, "MAW::initialize could not find\n" |
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< |
"\tMAW parameters for %s - %s interaction.\n", |
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< |
atypes.first->getName().c_str(), |
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< |
atypes.second->getName().c_str()); |
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< |
painCave.severity = OPENMD_ERROR; |
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< |
painCave.isFatal = 1; |
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< |
simError(); |
| 77 |
< |
} |
| 78 |
< |
|
| 79 |
< |
MAWData* mawData = dynamic_cast<MAWData*>(data); |
| 80 |
< |
if (mawData == NULL) { |
| 67 |
> |
keys = nbiTypes->getKeys(j); |
| 68 |
> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
| 69 |
> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
| 70 |
> |
|
| 71 |
> |
MAWInteractionType* mit = dynamic_cast<MAWInteractionType*>(nbt); |
| 72 |
> |
|
| 73 |
> |
if (mit == NULL) { |
| 74 |
|
sprintf( painCave.errMsg, |
| 75 |
< |
"MAW::initialize could not convert GenericData to\n" |
| 76 |
< |
"\tMAWData for %s - %s interaction.\n", |
| 77 |
< |
atypes.first->getName().c_str(), |
| 78 |
< |
atypes.second->getName().c_str()); |
| 75 |
> |
"MAW::initialize could not convert NonBondedInteractionType\n" |
| 76 |
> |
"\tto MAWInteractionType for %s - %s interaction.\n", |
| 77 |
> |
at1->getName().c_str(), |
| 78 |
> |
at2->getName().c_str()); |
| 79 |
|
painCave.severity = OPENMD_ERROR; |
| 80 |
|
painCave.isFatal = 1; |
| 81 |
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simError(); |
| 82 |
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} |
| 83 |
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|
| 84 |
< |
MAWParam mawParam = mawData->getData(); |
| 85 |
< |
|
| 86 |
< |
RealType De = mawParam.De; |
| 87 |
< |
RealType beta = mawParam.beta; |
| 88 |
< |
RealType Re = mawParam.Re; |
| 96 |
< |
RealType ca1 = mawParam.ca1; |
| 97 |
< |
RealType cb1 = mawParam.cb1; |
| 84 |
> |
RealType De = mit->getD(); |
| 85 |
> |
RealType beta = mit->getBeta(); |
| 86 |
> |
RealType Re = mit->getR(); |
| 87 |
> |
RealType ca1 = mit->getCA1(); |
| 88 |
> |
RealType cb1 = mit->getCB1(); |
| 89 |
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|
| 90 |
< |
addExplicitInteraction(atypes.first, atypes.second, |
| 90 |
> |
addExplicitInteraction(at1, at2, |
| 91 |
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De, beta, Re, ca1, cb1); |
| 92 |
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} |
| 93 |
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} |
| 115 |
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} |
| 116 |
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} |
| 117 |
|
|
| 118 |
< |
void MAW::calcForce(InteractionData idat) { |
| 118 |
> |
void MAW::calcForce(InteractionData &idat) { |
| 119 |
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|
| 120 |
|
if (!initialized_) initialize(); |
| 121 |
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|
| 131 |
– |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 122 |
|
map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it; |
| 123 |
< |
it = MixingMap.find(key); |
| 123 |
> |
it = MixingMap.find( idat.atypes ); |
| 124 |
|
if (it != MixingMap.end()) { |
| 125 |
|
MAWInteractionData mixer = (*it).second; |
| 126 |
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|
| 135 |
|
RealType ca1 = mixer.ca1; |
| 136 |
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RealType cb1 = mixer.cb1; |
| 137 |
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|
| 138 |
< |
bool j_is_Metal = idat.atype2->isMetal(); |
| 138 |
> |
bool j_is_Metal = idat.atypes.second->isMetal(); |
| 139 |
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|
| 140 |
|
Vector3d r; |
| 141 |
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RotMat3x3d Atrans; |
| 142 |
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if (j_is_Metal) { |
| 143 |
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// rotate the inter-particle separation into the two different |
| 144 |
|
// body-fixed coordinate systems: |
| 145 |
< |
r = idat.A1 * idat.d; |
| 146 |
< |
Atrans = idat.A1.transpose(); |
| 145 |
> |
r = *(idat.A1) * *(idat.d); |
| 146 |
> |
Atrans = idat.A1->transpose(); |
| 147 |
|
} else { |
| 148 |
|
// negative sign because this is the vector from j to i: |
| 149 |
< |
r = -idat.A2 * idat.d; |
| 150 |
< |
Atrans = idat.A2.transpose(); |
| 149 |
> |
r = -*(idat.A2) * *(idat.d); |
| 150 |
> |
Atrans = idat.A2->transpose(); |
| 151 |
|
} |
| 152 |
|
|
| 153 |
|
// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
| 154 |
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|
| 155 |
< |
RealType expt = -beta*(idat.rij - R_e); |
| 155 |
> |
RealType expt = -beta*( *(idat.rij) - R_e); |
| 156 |
|
RealType expfnc = exp(expt); |
| 157 |
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RealType expfnc2 = expfnc*expfnc; |
| 158 |
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|
| 163 |
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myPot = D_e * (expfnc2 - 2.0 * expfnc); |
| 164 |
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myDeriv = 2.0 * D_e * beta * (expfnc - expfnc2); |
| 165 |
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|
| 166 |
< |
if (MAW::shiftedPot_ || MAW::shiftedFrc_) { |
| 167 |
< |
exptC = -beta*(idat.rcut - R_e); |
| 166 |
> |
if (idat.shiftedPot || idat.shiftedForce) { |
| 167 |
> |
exptC = -beta*( *(idat.rcut) - R_e); |
| 168 |
|
expfncC = exp(exptC); |
| 169 |
|
expfnc2C = expfncC*expfncC; |
| 170 |
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} |
| 171 |
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|
| 172 |
< |
if (MAW::shiftedPot_) { |
| 172 |
> |
if (idat.shiftedPot) { |
| 173 |
|
myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
| 174 |
|
myDerivC = 0.0; |
| 175 |
< |
} else if (MAW::shiftedFrc_) { |
| 175 |
> |
} else if (idat.shiftedForce) { |
| 176 |
|
myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
| 177 |
|
myDerivC = 2.0 * D_e * beta * (expfnc2C - expfnc2C); |
| 178 |
< |
myPotC += myDerivC * (idat.rij - idat.rcut); |
| 178 |
> |
myPotC += myDerivC * ( *(idat.rij) - *(idat.rcut) ); |
| 179 |
|
} else { |
| 180 |
|
myPotC = 0.0; |
| 181 |
|
myDerivC = 0.0; |
| 185 |
|
RealType y = r.y(); |
| 186 |
|
RealType z = r.z(); |
| 187 |
|
RealType x2 = x * x; |
| 198 |
– |
RealType y2 = y * y; |
| 188 |
|
RealType z2 = z * z; |
| 189 |
|
|
| 190 |
< |
RealType r3 = idat.r2 * idat.rij; |
| 191 |
< |
RealType r4 = idat.r2 * idat.r2; |
| 190 |
> |
RealType r3 = *(idat.r2) * *(idat.rij) ; |
| 191 |
> |
RealType r4 = *(idat.r2) * *(idat.r2); |
| 192 |
|
|
| 193 |
|
// angular modulation of morse part of potential to approximate |
| 194 |
|
// the squares of the two HOMO lone pair orbitals in water: |
| 206 |
|
// Vmorse(r)*[a*x2/r2 + b*z/r + (1-a-b)] |
| 207 |
|
|
| 208 |
|
RealType Vmorse = (myPot - myPotC); |
| 209 |
< |
RealType Vang = ca1 * x2 / idat.r2 + cb1 * z / idat.rij + (0.8 - ca1 / 3.0); |
| 210 |
< |
|
| 211 |
< |
RealType pot_temp = idat.vdwMult * Vmorse * Vang; |
| 212 |
< |
idat.vpair += pot_temp; |
| 213 |
< |
idat.pot += idat.sw * pot_temp; |
| 209 |
> |
RealType Vang = ca1 * x2 / *(idat.r2) + |
| 210 |
> |
cb1 * z / *(idat.rij) + (0.8 - ca1 / 3.0); |
| 211 |
> |
|
| 212 |
> |
RealType pot_temp = *(idat.vdwMult) * Vmorse * Vang; |
| 213 |
> |
*(idat.vpair) += pot_temp; |
| 214 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 215 |
|
|
| 216 |
< |
Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / idat.rij; |
| 227 |
< |
|
| 228 |
< |
Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / idat.r2 - cb1 * x * z / r3, |
| 229 |
< |
-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3, |
| 230 |
< |
-2.0 * ca1 * x2 * z / r4 + cb1 / idat.rij - cb1 * z2 / r3); |
| 216 |
> |
Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / *(idat.rij) ; |
| 217 |
|
|
| 218 |
+ |
Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / *(idat.r2) - cb1 * x * z / r3, |
| 219 |
+ |
-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3, |
| 220 |
+ |
-2.0 * ca1 * x2 * z / r4 + cb1 / *(idat.rij) - cb1 * z2 / r3); |
| 221 |
+ |
|
| 222 |
|
// chain rule to put these back on x, y, z |
| 223 |
|
|
| 224 |
|
Vector3d dvdr = Vang * dVmorsedr + Vmorse * dVangdr; |
| 226 |
|
// Torques for Vang using method of Price: |
| 227 |
|
// S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984). |
| 228 |
|
|
| 229 |
< |
Vector3d dVangdu = Vector3d(cb1 * y / idat.rij, |
| 230 |
< |
2.0 * ca1 * x * z / idat.r2 - cb1 * x / idat.rij, |
| 231 |
< |
-2.0 * ca1 * y * x / idat.r2); |
| 229 |
> |
Vector3d dVangdu = Vector3d(cb1 * y / *(idat.rij) , |
| 230 |
> |
2.0 * ca1 * x * z / *(idat.r2) - cb1 * x / *(idat.rij), |
| 231 |
> |
-2.0 * ca1 * y * x / *(idat.r2)); |
| 232 |
|
|
| 233 |
|
// do the torques first since they are easy: |
| 234 |
|
// remember that these are still in the body fixed axes |
| 235 |
|
|
| 236 |
< |
Vector3d trq = idat.vdwMult * Vmorse * dVangdu * idat.sw; |
| 236 |
> |
Vector3d trq = *(idat.vdwMult) * Vmorse * dVangdu * *(idat.sw); |
| 237 |
|
|
| 238 |
|
// go back to lab frame using transpose of rotation matrix: |
| 239 |
|
|
| 240 |
|
if (j_is_Metal) { |
| 241 |
< |
idat.t1 += Atrans * trq; |
| 241 |
> |
*(idat.t1) += Atrans * trq; |
| 242 |
|
} else { |
| 243 |
< |
idat.t2 += Atrans * trq; |
| 243 |
> |
*(idat.t2) += Atrans * trq; |
| 244 |
|
} |
| 245 |
|
|
| 246 |
|
// Now, on to the forces (still in body frame of water) |
| 247 |
|
|
| 248 |
< |
Vector3d ftmp = idat.vdwMult * idat.sw * dvdr; |
| 248 |
> |
Vector3d ftmp = *(idat.vdwMult) * *(idat.sw) * dvdr; |
| 249 |
|
|
| 250 |
|
// rotate the terms back into the lab frame: |
| 251 |
|
Vector3d flab; |
| 255 |
|
flab = - Atrans * ftmp; |
| 256 |
|
} |
| 257 |
|
|
| 258 |
< |
idat.f1 += flab; |
| 258 |
> |
*(idat.f1) += flab; |
| 259 |
|
} |
| 260 |
|
return; |
| 261 |
|
|
| 262 |
|
} |
| 263 |
|
|
| 264 |
< |
RealType MAW::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 264 |
> |
RealType MAW::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 265 |
|
if (!initialized_) initialize(); |
| 276 |
– |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 266 |
|
map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it; |
| 267 |
< |
it = MixingMap.find(key); |
| 267 |
> |
it = MixingMap.find(atypes); |
| 268 |
|
if (it == MixingMap.end()) |
| 269 |
|
return 0.0; |
| 270 |
|
else { |
