| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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 |
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#include "nonbonded/RepulsivePower.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
< |
#include "types/NonBondedInteractionType.hpp" |
| 49 |
> |
#include "types/RepulsivePowerInteractionType.hpp" |
| 50 |
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|
| 51 |
|
using namespace std; |
| 52 |
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|
| 57 |
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|
| 58 |
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void RepulsivePower::initialize() { |
| 59 |
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|
| 60 |
+ |
RPtypes.clear(); |
| 61 |
+ |
RPtids.clear(); |
| 62 |
+ |
MixingMap.clear(); |
| 63 |
+ |
RPtids.resize( forceField_->getNAtomType(), -1); |
| 64 |
+ |
|
| 65 |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 66 |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 67 |
+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
| 68 |
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NonBondedInteractionType* nbt; |
| 69 |
+ |
int rptid1, rptid2; |
| 70 |
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|
| 71 |
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 72 |
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nbt = nbiTypes->nextType(j)) { |
| 73 |
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|
| 74 |
|
if (nbt->isRepulsivePower()) { |
| 75 |
< |
|
| 76 |
< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 77 |
< |
|
| 78 |
< |
GenericData* data = nbt->getPropertyByName("RepulsivePower"); |
| 79 |
< |
if (data == NULL) { |
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< |
sprintf( painCave.errMsg, "RepulsivePower::initialize could not\n" |
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< |
"\tfind RepulsivePower parameters for %s - %s interaction.\n", |
| 82 |
< |
atypes.first->getName().c_str(), |
| 83 |
< |
atypes.second->getName().c_str()); |
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< |
painCave.severity = OPENMD_ERROR; |
| 77 |
< |
painCave.isFatal = 1; |
| 78 |
< |
simError(); |
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> |
keys = nbiTypes->getKeys(j); |
| 76 |
> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
| 77 |
> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
| 78 |
> |
|
| 79 |
> |
int atid1 = at1->getIdent(); |
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> |
if (RPtids[atid1] == -1) { |
| 81 |
> |
rptid1 = RPtypes.size(); |
| 82 |
> |
RPtypes.insert(atid1); |
| 83 |
> |
RPtids[atid1] = rptid1; |
| 84 |
|
} |
| 85 |
< |
|
| 86 |
< |
RepulsivePowerData* rpData = dynamic_cast<RepulsivePowerData*>(data); |
| 87 |
< |
if (rpData == NULL) { |
| 85 |
> |
int atid2 = at2->getIdent(); |
| 86 |
> |
if (RPtids[atid2] == -1) { |
| 87 |
> |
rptid2 = RPtypes.size(); |
| 88 |
> |
RPtypes.insert(atid2); |
| 89 |
> |
RPtids[atid2] = rptid2; |
| 90 |
> |
} |
| 91 |
> |
|
| 92 |
> |
RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt); |
| 93 |
> |
if (rpit == NULL) { |
| 94 |
|
sprintf( painCave.errMsg, |
| 95 |
< |
"RepulsivePower::initialize could not convert GenericData\n" |
| 96 |
< |
"\tto RepulsivePowerData for %s - %s interaction.\n", |
| 97 |
< |
atypes.first->getName().c_str(), |
| 98 |
< |
atypes.second->getName().c_str()); |
| 95 |
> |
"RepulsivePower::initialize could not convert NonBondedInteractionType\n" |
| 96 |
> |
"\tto RepulsivePowerInteractionType for %s - %s interaction.\n", |
| 97 |
> |
at1->getName().c_str(), |
| 98 |
> |
at2->getName().c_str()); |
| 99 |
|
painCave.severity = OPENMD_ERROR; |
| 100 |
|
painCave.isFatal = 1; |
| 101 |
|
simError(); |
| 102 |
|
} |
| 103 |
|
|
| 104 |
< |
RepulsivePowerParam rpParam = rpData->getData(); |
| 104 |
> |
RealType sigma = rpit->getSigma(); |
| 105 |
> |
RealType epsilon = rpit->getEpsilon(); |
| 106 |
> |
int nRep = rpit->getNrep(); |
| 107 |
|
|
| 108 |
< |
RealType sigma = rpParam.sigma; |
| 96 |
< |
RealType epsilon = rpParam.epsilon; |
| 97 |
< |
int nRep = rpParam.nRep; |
| 98 |
< |
|
| 99 |
< |
addExplicitInteraction(atypes.first, atypes.second, |
| 100 |
< |
sigma, epsilon, nRep); |
| 108 |
> |
addExplicitInteraction(at1, at2, sigma, epsilon, nRep); |
| 109 |
|
} |
| 110 |
|
} |
| 111 |
|
initialized_ = true; |
| 123 |
|
mixer.sigmai = 1.0 / mixer.sigma; |
| 124 |
|
mixer.nRep = nRep; |
| 125 |
|
|
| 126 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 127 |
< |
key1 = make_pair(atype1, atype2); |
| 128 |
< |
key2 = make_pair(atype2, atype1); |
| 126 |
> |
int rptid1 = RPtids[atype1->getIdent()]; |
| 127 |
> |
int rptid2 = RPtids[atype2->getIdent()]; |
| 128 |
> |
int nRP = RPtypes.size(); |
| 129 |
> |
|
| 130 |
> |
MixingMap.resize(nRP); |
| 131 |
> |
MixingMap[rptid1].resize(nRP); |
| 132 |
|
|
| 133 |
< |
MixingMap[key1] = mixer; |
| 134 |
< |
if (key2 != key1) { |
| 135 |
< |
MixingMap[key2] = mixer; |
| 133 |
> |
MixingMap[rptid1][rptid2] = mixer; |
| 134 |
> |
if (rptid2 != rptid1) { |
| 135 |
> |
MixingMap[rptid2].resize(nRP); |
| 136 |
> |
MixingMap[rptid2][rptid1] = mixer; |
| 137 |
|
} |
| 138 |
|
} |
| 139 |
|
|
| 141 |
|
|
| 142 |
|
if (!initialized_) initialize(); |
| 143 |
|
|
| 144 |
< |
map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it; |
| 145 |
< |
it = MixingMap.find( idat.atypes ); |
| 146 |
< |
|
| 147 |
< |
if (it != MixingMap.end()) { |
| 148 |
< |
|
| 149 |
< |
RPInteractionData mixer = (*it).second; |
| 150 |
< |
RealType sigmai = mixer.sigmai; |
| 151 |
< |
RealType epsilon = mixer.epsilon; |
| 152 |
< |
int nRep = mixer.nRep; |
| 153 |
< |
|
| 154 |
< |
RealType ros; |
| 155 |
< |
RealType rcos; |
| 156 |
< |
RealType myPot = 0.0; |
| 157 |
< |
RealType myPotC = 0.0; |
| 158 |
< |
RealType myDeriv = 0.0; |
| 159 |
< |
RealType myDerivC = 0.0; |
| 160 |
< |
|
| 161 |
< |
ros = *(idat.rij) * sigmai; |
| 162 |
< |
|
| 163 |
< |
getNRepulsionFunc(ros, nRep, myPot, myDeriv); |
| 164 |
< |
|
| 165 |
< |
if (idat.shiftedPot) { |
| 166 |
< |
rcos = *(idat.rcut) * sigmai; |
| 167 |
< |
getNRepulsionFunc(rcos, nRep, myPotC, myDerivC); |
| 168 |
< |
myDerivC = 0.0; |
| 169 |
< |
} else if (idat.shiftedForce) { |
| 170 |
< |
rcos = *(idat.rcut) * sigmai; |
| 159 |
< |
getNRepulsionFunc(rcos, nRep, myPotC, myDerivC); |
| 160 |
< |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
| 161 |
< |
} else { |
| 162 |
< |
myPotC = 0.0; |
| 163 |
< |
myDerivC = 0.0; |
| 164 |
< |
} |
| 165 |
< |
|
| 166 |
< |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 167 |
< |
*(idat.vpair) += pot_temp; |
| 168 |
< |
|
| 169 |
< |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 170 |
< |
myDerivC)*sigmai; |
| 171 |
< |
|
| 172 |
< |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 173 |
< |
*(idat.f1) = *(idat.d) * dudr / *(idat.rij); |
| 144 |
> |
RPInteractionData &mixer = MixingMap[RPtids[idat.atid1]][RPtids[idat.atid2]]; |
| 145 |
> |
RealType sigmai = mixer.sigmai; |
| 146 |
> |
RealType epsilon = mixer.epsilon; |
| 147 |
> |
int nRep = mixer.nRep; |
| 148 |
> |
|
| 149 |
> |
RealType ros; |
| 150 |
> |
RealType rcos; |
| 151 |
> |
RealType myPot = 0.0; |
| 152 |
> |
RealType myPotC = 0.0; |
| 153 |
> |
RealType myDeriv = 0.0; |
| 154 |
> |
RealType myDerivC = 0.0; |
| 155 |
> |
|
| 156 |
> |
ros = *(idat.rij) * sigmai; |
| 157 |
> |
|
| 158 |
> |
getNRepulsionFunc(ros, nRep, myPot, myDeriv); |
| 159 |
> |
|
| 160 |
> |
if (idat.shiftedPot) { |
| 161 |
> |
rcos = *(idat.rcut) * sigmai; |
| 162 |
> |
getNRepulsionFunc(rcos, nRep, myPotC, myDerivC); |
| 163 |
> |
myDerivC = 0.0; |
| 164 |
> |
} else if (idat.shiftedForce) { |
| 165 |
> |
rcos = *(idat.rcut) * sigmai; |
| 166 |
> |
getNRepulsionFunc(rcos, nRep, myPotC, myDerivC); |
| 167 |
> |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
| 168 |
> |
} else { |
| 169 |
> |
myPotC = 0.0; |
| 170 |
> |
myDerivC = 0.0; |
| 171 |
|
} |
| 172 |
+ |
|
| 173 |
+ |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 174 |
+ |
*(idat.vpair) += pot_temp; |
| 175 |
+ |
|
| 176 |
+ |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 177 |
+ |
myDerivC)*sigmai; |
| 178 |
+ |
|
| 179 |
+ |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 180 |
+ |
*(idat.f1) = *(idat.d) * dudr / *(idat.rij); |
| 181 |
+ |
|
| 182 |
|
return; |
| 183 |
|
} |
| 184 |
|
|
| 185 |
< |
void RepulsivePower::getNRepulsionFunc(RealType r, int n, RealType &pot, RealType &deriv) { |
| 185 |
> |
void RepulsivePower::getNRepulsionFunc(const RealType &r, int &n, RealType &pot, RealType &deriv) { |
| 186 |
|
|
| 187 |
|
RealType ri = 1.0 / r; |
| 188 |
|
RealType rin = pow(ri, n); |
| 197 |
|
|
| 198 |
|
RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 199 |
|
if (!initialized_) initialize(); |
| 200 |
< |
map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it; |
| 201 |
< |
it = MixingMap.find(atypes); |
| 202 |
< |
if (it == MixingMap.end()) |
| 203 |
< |
return 0.0; |
| 204 |
< |
else { |
| 205 |
< |
RPInteractionData mixer = (*it).second; |
| 200 |
> |
|
| 201 |
> |
int atid1 = atypes.first->getIdent(); |
| 202 |
> |
int atid2 = atypes.second->getIdent(); |
| 203 |
> |
int rptid1 = RPtids[atid1]; |
| 204 |
> |
int rptid2 = RPtids[atid2]; |
| 205 |
> |
|
| 206 |
> |
if (rptid1 == -1 || rptid2 == -1) return 0.0; |
| 207 |
> |
else { |
| 208 |
> |
RPInteractionData mixer = MixingMap[rptid1][rptid2]; |
| 209 |
|
return 2.5 * mixer.sigma; |
| 210 |
|
} |
| 211 |
< |
} |
| 202 |
< |
|
| 211 |
> |
} |
| 212 |
|
} |
| 213 |
|
|
