| 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 |
|
#include "nonbonded/LJ.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
+ |
#include "types/LennardJonesAdapter.hpp" |
| 50 |
+ |
#include "types/LennardJonesInteractionType.hpp" |
| 51 |
|
|
| 52 |
|
namespace OpenMD { |
| 53 |
|
|
| 54 |
< |
LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), |
| 52 |
< |
shiftedFrc_(false), forceField_(NULL) {} |
| 54 |
> |
LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} |
| 55 |
|
|
| 56 |
< |
LJParam LJ::getLJParam(AtomType* atomType) { |
| 55 |
< |
|
| 56 |
< |
// Do sanity checking on the AtomType we were passed before |
| 57 |
< |
// building any data structures: |
| 58 |
< |
if (!atomType->isLennardJones()) { |
| 59 |
< |
sprintf( painCave.errMsg, |
| 60 |
< |
"LJ::getLJParam was passed an atomType (%s) that does not\n" |
| 61 |
< |
"\tappear to be a Lennard-Jones atom.\n", |
| 62 |
< |
atomType->getName().c_str()); |
| 63 |
< |
painCave.severity = OPENMD_ERROR; |
| 64 |
< |
painCave.isFatal = 1; |
| 65 |
< |
simError(); |
| 66 |
< |
} |
| 67 |
< |
|
| 68 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 69 |
< |
if (data == NULL) { |
| 70 |
< |
sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n" |
| 71 |
< |
"\tparameters for atomType %s.\n", atomType->getName().c_str()); |
| 72 |
< |
painCave.severity = OPENMD_ERROR; |
| 73 |
< |
painCave.isFatal = 1; |
| 74 |
< |
simError(); |
| 75 |
< |
} |
| 76 |
< |
|
| 77 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 78 |
< |
if (ljData == NULL) { |
| 79 |
< |
sprintf( painCave.errMsg, |
| 80 |
< |
"LJ::getLJParam could not convert GenericData to LJParam for\n" |
| 81 |
< |
"\tatom type %s\n", atomType->getName().c_str()); |
| 82 |
< |
painCave.severity = OPENMD_ERROR; |
| 83 |
< |
painCave.isFatal = 1; |
| 84 |
< |
simError(); |
| 85 |
< |
} |
| 86 |
< |
|
| 87 |
< |
return ljData->getData(); |
| 88 |
< |
} |
| 56 |
> |
RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
| 57 |
|
|
| 58 |
< |
RealType LJ::getSigma(AtomType* atomType) { |
| 59 |
< |
LJParam ljParam = getLJParam(atomType); |
| 60 |
< |
return ljParam.sigma; |
| 61 |
< |
} |
| 94 |
< |
|
| 95 |
< |
RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
| 96 |
< |
RealType sigma1 = getSigma(atomType1); |
| 97 |
< |
RealType sigma2 = getSigma(atomType2); |
| 58 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
| 59 |
> |
LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
| 60 |
> |
RealType sigma1 = lja1.getSigma(); |
| 61 |
> |
RealType sigma2 = lja2.getSigma(); |
| 62 |
|
|
| 63 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 64 |
|
string DistanceMix = fopts.getDistanceMixingRule(); |
| 70 |
|
return 0.5 * (sigma1 + sigma2); |
| 71 |
|
} |
| 72 |
|
|
| 73 |
< |
RealType LJ::getEpsilon(AtomType* atomType) { |
| 74 |
< |
LJParam ljParam = getLJParam(atomType); |
| 75 |
< |
return ljParam.epsilon; |
| 76 |
< |
} |
| 77 |
< |
|
| 78 |
< |
RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
| 115 |
< |
RealType epsilon1 = getEpsilon(atomType1); |
| 116 |
< |
RealType epsilon2 = getEpsilon(atomType2); |
| 73 |
> |
RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
| 74 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
| 75 |
> |
LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
| 76 |
> |
|
| 77 |
> |
RealType epsilon1 = lja1.getEpsilon(); |
| 78 |
> |
RealType epsilon2 = lja2.getEpsilon(); |
| 79 |
|
return sqrt(epsilon1 * epsilon2); |
| 80 |
|
} |
| 81 |
|
|
| 82 |
|
void LJ::initialize() { |
| 121 |
– |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 122 |
– |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 123 |
– |
AtomType* at; |
| 83 |
|
|
| 84 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 85 |
< |
at = atomTypes->nextType(i)) { |
| 86 |
< |
|
| 87 |
< |
if (at->isLennardJones()) |
| 88 |
< |
addType(at); |
| 84 |
> |
LJtypes.clear(); |
| 85 |
> |
LJtids.clear(); |
| 86 |
> |
MixingMap.clear(); |
| 87 |
> |
nLJ_ = 0; |
| 88 |
> |
|
| 89 |
> |
LJtids.resize( forceField_->getNAtomType(), -1); |
| 90 |
> |
|
| 91 |
> |
set<AtomType*>::iterator at; |
| 92 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 93 |
> |
if ((*at)->isLennardJones()) nLJ_++; |
| 94 |
|
} |
| 95 |
|
|
| 96 |
+ |
MixingMap.resize(nLJ_); |
| 97 |
+ |
|
| 98 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 99 |
+ |
if ((*at)->isLennardJones()) addType(*at); |
| 100 |
+ |
} |
| 101 |
+ |
|
| 102 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 103 |
|
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 104 |
|
NonBondedInteractionType* nbt; |
| 105 |
+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
| 106 |
|
|
| 107 |
|
for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 108 |
|
nbt = nbiTypes->nextType(j)) { |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
if (nbt->isLennardJones()) { |
| 111 |
< |
|
| 112 |
< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 113 |
< |
|
| 114 |
< |
GenericData* data = nbt->getPropertyByName("LennardJones"); |
| 115 |
< |
if (data == NULL) { |
| 116 |
< |
sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n" |
| 117 |
< |
"\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) { |
| 111 |
> |
keys = nbiTypes->getKeys(j); |
| 112 |
> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
| 113 |
> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
| 114 |
> |
|
| 115 |
> |
LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt); |
| 116 |
> |
|
| 117 |
> |
if (ljit == NULL) { |
| 118 |
|
sprintf( painCave.errMsg, |
| 119 |
< |
"LJ::rebuildMixingMap could not convert GenericData to\n" |
| 120 |
< |
"\tLJParam for %s - %s interaction.\n", |
| 121 |
< |
atypes.first->getName().c_str(), |
| 122 |
< |
atypes.second->getName().c_str()); |
| 119 |
> |
"LJ::initialize could not convert NonBondedInteractionType\n" |
| 120 |
> |
"\tto LennardJonesInteractionType for %s - %s interaction.\n", |
| 121 |
> |
at1->getName().c_str(), |
| 122 |
> |
at2->getName().c_str()); |
| 123 |
|
painCave.severity = OPENMD_ERROR; |
| 124 |
|
painCave.isFatal = 1; |
| 125 |
|
simError(); |
| 126 |
|
} |
| 165 |
– |
|
| 166 |
– |
LJParam ljParam = ljData->getData(); |
| 127 |
|
|
| 128 |
< |
RealType sigma = ljParam.sigma; |
| 129 |
< |
RealType epsilon = ljParam.epsilon; |
| 130 |
< |
|
| 171 |
< |
addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon); |
| 128 |
> |
RealType sigma = ljit->getSigma(); |
| 129 |
> |
RealType epsilon = ljit->getEpsilon(); |
| 130 |
> |
addExplicitInteraction(at1, at2, sigma, epsilon); |
| 131 |
|
} |
| 132 |
|
} |
| 133 |
|
initialized_ = true; |
| 134 |
|
} |
| 176 |
– |
|
| 135 |
|
|
| 136 |
|
|
| 137 |
|
void LJ::addType(AtomType* atomType){ |
| 138 |
< |
RealType sigma1 = getSigma(atomType); |
| 139 |
< |
RealType epsilon1 = getEpsilon(atomType); |
| 138 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
| 139 |
> |
|
| 140 |
> |
RealType sigma1 = lja1.getSigma(); |
| 141 |
> |
RealType epsilon1 = lja1.getEpsilon(); |
| 142 |
|
|
| 143 |
|
// add it to the map: |
| 144 |
< |
AtomTypeProperties atp = atomType->getATP(); |
| 145 |
< |
|
| 146 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 147 |
< |
ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 144 |
> |
int atid = atomType->getIdent(); |
| 145 |
> |
int ljtid = LJtypes.size(); |
| 146 |
> |
|
| 147 |
> |
pair<set<int>::iterator,bool> ret; |
| 148 |
> |
ret = LJtypes.insert( atid ); |
| 149 |
|
if (ret.second == false) { |
| 150 |
|
sprintf( painCave.errMsg, |
| 151 |
|
"LJ already had a previous entry with ident %d\n", |
| 152 |
< |
atp.ident); |
| 152 |
> |
atid) ; |
| 153 |
|
painCave.severity = OPENMD_INFO; |
| 154 |
|
painCave.isFatal = 0; |
| 155 |
|
simError(); |
| 156 |
|
} |
| 157 |
< |
|
| 157 |
> |
|
| 158 |
> |
LJtids[atid] = ljtid; |
| 159 |
> |
MixingMap[ljtid].resize( nLJ_ ); |
| 160 |
> |
|
| 161 |
|
// Now, iterate over all known types and add to the mixing map: |
| 162 |
|
|
| 163 |
< |
std::map<int, AtomType*>::iterator it; |
| 164 |
< |
for( it = LJMap.begin(); it != LJMap.end(); ++it) { |
| 201 |
< |
|
| 202 |
< |
AtomType* atype2 = (*it).second; |
| 163 |
> |
std::set<int>::iterator it; |
| 164 |
> |
for( it = LJtypes.begin(); it != LJtypes.end(); ++it) { |
| 165 |
|
|
| 166 |
+ |
int ljtid2 = LJtids[ (*it) ]; |
| 167 |
+ |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 168 |
+ |
|
| 169 |
|
LJInteractionData mixer; |
| 170 |
|
mixer.sigma = getSigma(atomType, atype2); |
| 171 |
|
mixer.epsilon = getEpsilon(atomType, atype2); |
| 172 |
|
mixer.sigmai = 1.0 / mixer.sigma; |
| 173 |
|
mixer.explicitlySet = false; |
| 174 |
+ |
MixingMap[ljtid2].resize( nLJ_ ); |
| 175 |
|
|
| 176 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 177 |
< |
key1 = std::make_pair(atomType, atype2); |
| 178 |
< |
key2 = std::make_pair(atype2, atomType); |
| 213 |
< |
|
| 214 |
< |
MixingMap[key1] = mixer; |
| 215 |
< |
if (key2 != key1) { |
| 216 |
< |
MixingMap[key2] = mixer; |
| 176 |
> |
MixingMap[ljtid][ljtid2] = mixer; |
| 177 |
> |
if (ljtid2 != ljtid) { |
| 178 |
> |
MixingMap[ljtid2][ljtid] = mixer; |
| 179 |
|
} |
| 180 |
|
} |
| 181 |
|
} |
| 182 |
|
|
| 183 |
|
void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){ |
| 184 |
|
|
| 223 |
– |
// in case these weren't already in the map |
| 224 |
– |
addType(atype1); |
| 225 |
– |
addType(atype2); |
| 226 |
– |
|
| 185 |
|
LJInteractionData mixer; |
| 186 |
|
mixer.sigma = sigma; |
| 187 |
|
mixer.epsilon = epsilon; |
| 188 |
|
mixer.sigmai = 1.0 / mixer.sigma; |
| 189 |
|
mixer.explicitlySet = true; |
| 190 |
|
|
| 191 |
< |
std::pair<AtomType*, AtomType*> key1, key2; |
| 192 |
< |
key1 = std::make_pair(atype1, atype2); |
| 193 |
< |
key2 = std::make_pair(atype2, atype1); |
| 191 |
> |
int atid1 = atype1->getIdent(); |
| 192 |
> |
int atid2 = atype2->getIdent(); |
| 193 |
> |
|
| 194 |
> |
int ljtid1, ljtid2; |
| 195 |
> |
|
| 196 |
> |
pair<set<int>::iterator,bool> ret; |
| 197 |
> |
ret = LJtypes.insert( atid1 ); |
| 198 |
> |
if (ret.second == false) { |
| 199 |
> |
// already had this type in the LJMap, just get the ljtid: |
| 200 |
> |
ljtid1 = LJtids[ atid1 ]; |
| 201 |
> |
} else { |
| 202 |
> |
// didn't already have it, so make a new one and assign it: |
| 203 |
> |
ljtid1 = nLJ_; |
| 204 |
> |
LJtids[atid1] = nLJ_; |
| 205 |
> |
nLJ_++; |
| 206 |
> |
} |
| 207 |
> |
|
| 208 |
> |
ret = LJtypes.insert( atid2 ); |
| 209 |
> |
if (ret.second == false) { |
| 210 |
> |
// already had this type in the LJMap, just get the ljtid: |
| 211 |
> |
ljtid2 = LJtids[ atid2 ]; |
| 212 |
> |
} else { |
| 213 |
> |
// didn't already have it, so make a new one and assign it: |
| 214 |
> |
ljtid2 = nLJ_; |
| 215 |
> |
LJtids[atid2] = nLJ_; |
| 216 |
> |
nLJ_++; |
| 217 |
> |
} |
| 218 |
|
|
| 219 |
< |
MixingMap[key1] = mixer; |
| 220 |
< |
if (key2 != key1) { |
| 221 |
< |
MixingMap[key2] = mixer; |
| 219 |
> |
MixingMap.resize(nLJ_); |
| 220 |
> |
MixingMap[ljtid1].resize(nLJ_); |
| 221 |
> |
|
| 222 |
> |
MixingMap[ljtid1][ljtid2] = mixer; |
| 223 |
> |
if (ljtid2 != ljtid1) { |
| 224 |
> |
MixingMap[ljtid2].resize(nLJ_); |
| 225 |
> |
MixingMap[ljtid2][ljtid1] = mixer; |
| 226 |
|
} |
| 227 |
|
} |
| 228 |
|
|
| 229 |
|
void LJ::calcForce(InteractionData &idat) { |
| 244 |
– |
|
| 230 |
|
if (!initialized_) initialize(); |
| 231 |
|
|
| 232 |
< |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 248 |
< |
it = MixingMap.find( idat.atypes ); |
| 249 |
< |
|
| 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 (shiftedPot_) { |
| 269 |
< |
rcos = *(idat.rcut) * sigmai; |
| 270 |
< |
getLJfunc(rcos, myPotC, myDerivC); |
| 271 |
< |
myDerivC = 0.0; |
| 272 |
< |
} else if (LJ::shiftedFrc_) { |
| 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 |
< |
} |
| 232 |
> |
LJInteractionData &mixer = MixingMap[LJtids[idat.atid1]][LJtids[idat.atid2]]; |
| 233 |
|
|
| 234 |
< |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 235 |
< |
*(idat.vpair) += pot_temp; |
| 236 |
< |
|
| 237 |
< |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 238 |
< |
myDerivC)*sigmai; |
| 239 |
< |
|
| 240 |
< |
(idat.pot)[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 241 |
< |
*(idat.f1) = *(idat.d) * dudr / *(idat.rij); |
| 234 |
> |
RealType sigmai = mixer.sigmai; |
| 235 |
> |
RealType epsilon = mixer.epsilon; |
| 236 |
> |
|
| 237 |
> |
RealType ros; |
| 238 |
> |
RealType rcos; |
| 239 |
> |
RealType myPot = 0.0; |
| 240 |
> |
RealType myPotC = 0.0; |
| 241 |
> |
RealType myDeriv = 0.0; |
| 242 |
> |
RealType myDerivC = 0.0; |
| 243 |
> |
|
| 244 |
> |
ros = *(idat.rij) * sigmai; |
| 245 |
> |
|
| 246 |
> |
getLJfunc(ros, myPot, myDeriv); |
| 247 |
> |
|
| 248 |
> |
if (idat.shiftedPot) { |
| 249 |
> |
rcos = *(idat.rcut) * sigmai; |
| 250 |
> |
getLJfunc(rcos, myPotC, myDerivC); |
| 251 |
> |
myDerivC = 0.0; |
| 252 |
> |
} else if (idat.shiftedForce) { |
| 253 |
> |
rcos = *(idat.rcut) * sigmai; |
| 254 |
> |
getLJfunc(rcos, myPotC, myDerivC); |
| 255 |
> |
myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
| 256 |
> |
} else { |
| 257 |
> |
myPotC = 0.0; |
| 258 |
> |
myDerivC = 0.0; |
| 259 |
|
} |
| 260 |
+ |
|
| 261 |
+ |
RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
| 262 |
+ |
*(idat.vpair) += pot_temp; |
| 263 |
+ |
|
| 264 |
+ |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
| 265 |
+ |
myDerivC)*sigmai; |
| 266 |
+ |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 267 |
+ |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 268 |
+ |
|
| 269 |
|
return; |
| 270 |
|
} |
| 271 |
|
|
| 286 |
|
|
| 287 |
|
RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 288 |
|
if (!initialized_) initialize(); |
| 289 |
< |
map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
| 290 |
< |
it = MixingMap.find(atypes); |
| 291 |
< |
if (it == MixingMap.end()) |
| 292 |
< |
return 0.0; |
| 293 |
< |
else { |
| 294 |
< |
LJInteractionData mixer = (*it).second; |
| 289 |
> |
|
| 290 |
> |
int atid1 = atypes.first->getIdent(); |
| 291 |
> |
int atid2 = atypes.second->getIdent(); |
| 292 |
> |
int ljtid1 = LJtids[atid1]; |
| 293 |
> |
int ljtid2 = LJtids[atid2]; |
| 294 |
> |
|
| 295 |
> |
if (ljtid1 == -1 || ljtid2 == -1) return 0.0; |
| 296 |
> |
else { |
| 297 |
> |
LJInteractionData mixer = MixingMap[ljtid1][ljtid2]; |
| 298 |
|
return 2.5 * mixer.sigma; |
| 299 |
|
} |
| 300 |
|
} |
| 301 |
< |
|
| 301 |
> |
|
| 302 |
|
} |
