| 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/Morse.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
< |
#include "types/NonBondedInteractionType.hpp" |
| 49 |
> |
#include "types/MorseInteractionType.hpp" |
| 50 |
|
|
| 51 |
|
using namespace std; |
| 52 |
|
|
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 55 |
< |
bool Morse::initialized_ = false; |
| 55 |
< |
bool Morse::shiftedPot_ = false; |
| 56 |
< |
bool Morse::shiftedFrc_ = false; |
| 57 |
< |
ForceField* Morse::forceField_ = NULL; |
| 58 |
< |
map<int, AtomType*> Morse::MorseMap; |
| 59 |
< |
map<pair<AtomType*, AtomType*>, MorseInteractionData> Morse::MixingMap; |
| 60 |
< |
map<string, MorseInteractionType> Morse::stringToEnumMap_; |
| 55 |
> |
Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL) {} |
| 56 |
|
|
| 62 |
– |
Morse* Morse::_instance = NULL; |
| 63 |
– |
|
| 64 |
– |
Morse* Morse::Instance() { |
| 65 |
– |
if (!_instance) { |
| 66 |
– |
_instance = new Morse(); |
| 67 |
– |
} |
| 68 |
– |
return _instance; |
| 69 |
– |
} |
| 70 |
– |
|
| 57 |
|
void Morse::initialize() { |
| 58 |
|
|
| 59 |
< |
stringToEnumMap_["shiftedMorse"] = shiftedMorse; |
| 60 |
< |
stringToEnumMap_["repulsiveMorse"] = repulsiveMorse; |
| 59 |
> |
Mtypes.clear(); |
| 60 |
> |
Mtids.clear(); |
| 61 |
> |
MixingMap.clear(); |
| 62 |
> |
Mtids.resize( forceField_->getNAtomType(), -1); |
| 63 |
|
|
| 64 |
|
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 65 |
|
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 66 |
+ |
ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
| 67 |
|
NonBondedInteractionType* nbt; |
| 68 |
+ |
int mtid1, mtid2; |
| 69 |
|
|
| 70 |
|
for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 71 |
|
nbt = nbiTypes->nextType(j)) { |
| 72 |
|
|
| 73 |
|
if (nbt->isMorse()) { |
| 74 |
< |
|
| 75 |
< |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 76 |
< |
|
| 77 |
< |
GenericData* data = nbt->getPropertyByName("Morse"); |
| 78 |
< |
if (data == NULL) { |
| 79 |
< |
sprintf( painCave.errMsg, "Morse::initialize could not find\n" |
| 80 |
< |
"\tMorse parameters for %s - %s interaction.\n", |
| 81 |
< |
atypes.first->getName().c_str(), |
| 82 |
< |
atypes.second->getName().c_str()); |
| 93 |
< |
painCave.severity = OPENMD_ERROR; |
| 94 |
< |
painCave.isFatal = 1; |
| 95 |
< |
simError(); |
| 74 |
> |
keys = nbiTypes->getKeys(j); |
| 75 |
> |
AtomType* at1 = forceField_->getAtomType(keys[0]); |
| 76 |
> |
AtomType* at2 = forceField_->getAtomType(keys[1]); |
| 77 |
> |
|
| 78 |
> |
int atid1 = at1->getIdent(); |
| 79 |
> |
if (Mtids[atid1] == -1) { |
| 80 |
> |
mtid1 = Mtypes.size(); |
| 81 |
> |
Mtypes.insert(atid1); |
| 82 |
> |
Mtids[atid1] = mtid1; |
| 83 |
|
} |
| 84 |
< |
|
| 85 |
< |
MorseData* morseData = dynamic_cast<MorseData*>(data); |
| 86 |
< |
if (morseData == NULL) { |
| 87 |
< |
sprintf( painCave.errMsg, |
| 88 |
< |
"Morse::initialize could not convert GenericData to\n" |
| 102 |
< |
"\tMorseData for %s - %s interaction.\n", |
| 103 |
< |
atypes.first->getName().c_str(), |
| 104 |
< |
atypes.second->getName().c_str()); |
| 105 |
< |
painCave.severity = OPENMD_ERROR; |
| 106 |
< |
painCave.isFatal = 1; |
| 107 |
< |
simError(); |
| 84 |
> |
int atid2 = at2->getIdent(); |
| 85 |
> |
if (Mtids[atid2] == -1) { |
| 86 |
> |
mtid2 = Mtypes.size(); |
| 87 |
> |
Mtypes.insert(atid2); |
| 88 |
> |
Mtids[atid2] = mtid2; |
| 89 |
|
} |
| 90 |
< |
|
| 91 |
< |
MorseParam morseParam = morseData->getData(); |
| 90 |
> |
|
| 91 |
> |
MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt); |
| 92 |
|
|
| 93 |
< |
RealType De = morseParam.De; |
| 113 |
< |
RealType Re = morseParam.Re; |
| 114 |
< |
RealType beta = morseParam.beta; |
| 115 |
< |
string interactionType = morseParam.interactionType; |
| 116 |
< |
|
| 117 |
< |
toUpper(interactionType); |
| 118 |
< |
map<string, MorseInteractionType>::iterator i; |
| 119 |
< |
i = stringToEnumMap_.find(interactionType); |
| 120 |
< |
if (i != stringToEnumMap_.end()) { |
| 121 |
< |
addExplicitInteraction(atypes.first, atypes.second, |
| 122 |
< |
De, Re, beta, i->second ); |
| 123 |
< |
} else { |
| 93 |
> |
if (mit == NULL) { |
| 94 |
|
sprintf( painCave.errMsg, |
| 95 |
< |
"Morse::initialize found unknown Morse interaction type\n" |
| 96 |
< |
"\t(%s) for %s - %s interaction.\n", |
| 97 |
< |
morseParam.interactionType.c_str(), |
| 98 |
< |
atypes.first->getName().c_str(), |
| 129 |
< |
atypes.second->getName().c_str()); |
| 95 |
> |
"Morse::initialize could not convert NonBondedInteractionType\n" |
| 96 |
> |
"\tto MorseInteractionType 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 |
+ |
RealType De = mit->getD(); |
| 105 |
+ |
RealType Re = mit->getR(); |
| 106 |
+ |
RealType beta = mit->getBeta(); |
| 107 |
+ |
|
| 108 |
+ |
MorseType variant = mit->getInteractionType(); |
| 109 |
+ |
addExplicitInteraction(at1, at2, De, Re, beta, variant ); |
| 110 |
|
} |
| 111 |
|
} |
| 112 |
|
initialized_ = true; |
| 114 |
|
|
| 115 |
|
void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
| 116 |
|
RealType De, RealType Re, RealType beta, |
| 117 |
< |
MorseInteractionType mit) { |
| 117 |
> |
MorseType mt) { |
| 118 |
|
|
| 143 |
– |
AtomTypeProperties atp = atype1->getATP(); |
| 144 |
– |
MorseMap.insert( pair<int, AtomType*>(atp.ident, atype1) ); |
| 145 |
– |
|
| 146 |
– |
atp = atype2->getATP(); |
| 147 |
– |
MorseMap.insert( pair<int, AtomType*>(atp.ident, atype2) ); |
| 148 |
– |
|
| 119 |
|
MorseInteractionData mixer; |
| 120 |
|
mixer.De = De; |
| 121 |
|
mixer.Re = Re; |
| 122 |
|
mixer.beta = beta; |
| 123 |
< |
mixer.interactionType = mit; |
| 123 |
> |
mixer.variant = mt; |
| 124 |
|
|
| 125 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 126 |
< |
key1 = make_pair(atype1, atype2); |
| 127 |
< |
key2 = make_pair(atype2, atype1); |
| 125 |
> |
int mtid1 = Mtids[atype1->getIdent()]; |
| 126 |
> |
int mtid2 = Mtids[atype2->getIdent()]; |
| 127 |
> |
int nM = Mtypes.size(); |
| 128 |
> |
|
| 129 |
> |
MixingMap.resize(nM); |
| 130 |
> |
MixingMap[mtid1].resize(nM); |
| 131 |
|
|
| 132 |
< |
MixingMap[key1] = mixer; |
| 133 |
< |
if (key2 != key1) { |
| 134 |
< |
MixingMap[key2] = mixer; |
| 132 |
> |
MixingMap[mtid1][mtid2] = mixer; |
| 133 |
> |
if (mtid2 != mtid1) { |
| 134 |
> |
MixingMap[mtid2].resize(nM); |
| 135 |
> |
MixingMap[mtid2][mtid1] = mixer; |
| 136 |
|
} |
| 137 |
|
} |
| 138 |
|
|
| 139 |
< |
void Morse::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 166 |
< |
RealType r, RealType r2, RealType rcut, RealType sw, |
| 167 |
< |
RealType vdwMult, RealType &vpair, RealType &pot, |
| 168 |
< |
Vector3d &f1) { |
| 139 |
> |
void Morse::calcForce(InteractionData &idat) { |
| 140 |
|
|
| 141 |
|
if (!initialized_) initialize(); |
| 142 |
|
|
| 143 |
+ |
MorseInteractionData &mixer = MixingMap[Mtids[idat.atid1]][Mtids[idat.atid2]]; |
| 144 |
+ |
|
| 145 |
|
RealType myPot = 0.0; |
| 146 |
|
RealType myPotC = 0.0; |
| 147 |
|
RealType myDeriv = 0.0; |
| 148 |
|
RealType myDerivC = 0.0; |
| 149 |
< |
|
| 177 |
< |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 178 |
< |
MorseInteractionData mixer = MixingMap[key]; |
| 179 |
< |
|
| 149 |
> |
|
| 150 |
|
RealType De = mixer.De; |
| 151 |
|
RealType Re = mixer.Re; |
| 152 |
|
RealType beta = mixer.beta; |
| 153 |
< |
MorseInteractionType interactionType = mixer.interactionType; |
| 154 |
< |
|
| 153 |
> |
MorseType variant = mixer.variant; |
| 154 |
> |
|
| 155 |
|
// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
| 156 |
|
|
| 157 |
< |
RealType expt = -beta*(r - Re); |
| 157 |
> |
RealType expt = -beta*( *(idat.rij) - Re); |
| 158 |
|
RealType expfnc = exp(expt); |
| 159 |
|
RealType expfnc2 = expfnc*expfnc; |
| 160 |
< |
|
| 160 |
> |
|
| 161 |
|
RealType exptC = 0.0; |
| 162 |
|
RealType expfncC = 0.0; |
| 163 |
|
RealType expfnc2C = 0.0; |
| 164 |
< |
|
| 165 |
< |
if (Morse::shiftedPot_ || Morse::shiftedFrc_) { |
| 166 |
< |
exptC = -beta*(rcut - Re); |
| 164 |
> |
|
| 165 |
> |
if (idat.shiftedPot || idat.shiftedForce) { |
| 166 |
> |
exptC = -beta*( *(idat.rcut) - Re); |
| 167 |
|
expfncC = exp(exptC); |
| 168 |
|
expfnc2C = expfncC*expfncC; |
| 169 |
|
} |
| 170 |
< |
|
| 171 |
< |
|
| 172 |
< |
switch(interactionType) { |
| 173 |
< |
case shiftedMorse : { |
| 174 |
< |
|
| 170 |
> |
|
| 171 |
> |
|
| 172 |
> |
switch(variant) { |
| 173 |
> |
case mtShifted : { |
| 174 |
> |
|
| 175 |
|
myPot = De * (expfnc2 - 2.0 * expfnc); |
| 176 |
|
myDeriv = 2.0 * De * beta * (expfnc - expfnc2); |
| 177 |
< |
|
| 178 |
< |
if (Morse::shiftedPot_) { |
| 177 |
> |
|
| 178 |
> |
if (idat.shiftedPot) { |
| 179 |
|
myPotC = De * (expfnc2C - 2.0 * expfncC); |
| 180 |
|
myDerivC = 0.0; |
| 181 |
< |
} else if (Morse::shiftedFrc_) { |
| 181 |
> |
} else if (idat.shiftedForce) { |
| 182 |
|
myPotC = De * (expfnc2C - 2.0 * expfncC); |
| 183 |
< |
myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C); |
| 184 |
< |
myPotC += myDerivC * (r - rcut); |
| 183 |
> |
myDerivC = 2.0 * De * beta * (expfncC - expfnc2C); |
| 184 |
> |
myPotC += myDerivC * ( *(idat.rij) - *(idat.rcut) ); |
| 185 |
|
} else { |
| 186 |
|
myPotC = 0.0; |
| 187 |
|
myDerivC = 0.0; |
| 188 |
|
} |
| 189 |
< |
|
| 189 |
> |
|
| 190 |
|
break; |
| 191 |
|
} |
| 192 |
< |
case repulsiveMorse : { |
| 193 |
< |
|
| 192 |
> |
case mtRepulsive : { |
| 193 |
> |
|
| 194 |
|
myPot = De * expfnc2; |
| 195 |
|
myDeriv = -2.0 * De * beta * expfnc2; |
| 196 |
< |
|
| 197 |
< |
if (Morse::shiftedPot_) { |
| 196 |
> |
|
| 197 |
> |
if (idat.shiftedPot) { |
| 198 |
|
myPotC = De * expfnc2C; |
| 199 |
|
myDerivC = 0.0; |
| 200 |
< |
} else if (Morse::shiftedFrc_) { |
| 200 |
> |
} else if (idat.shiftedForce) { |
| 201 |
|
myPotC = De * expfnc2C; |
| 202 |
|
myDerivC = -2.0 * De * beta * expfnc2C; |
| 203 |
< |
myPotC += myDerivC * (r - rcut); |
| 203 |
> |
myPotC += myDerivC * ( *(idat.rij) - *(idat.rcut)); |
| 204 |
|
} else { |
| 205 |
|
myPotC = 0.0; |
| 206 |
|
myDerivC = 0.0; |
| 207 |
|
} |
| 208 |
< |
|
| 208 |
> |
|
| 209 |
|
break; |
| 210 |
|
} |
| 211 |
+ |
case mtUnknown: { |
| 212 |
+ |
// don't know what to do so don't do anything |
| 213 |
+ |
break; |
| 214 |
|
} |
| 215 |
+ |
} |
| 216 |
+ |
|
| 217 |
|
|
| 218 |
< |
RealType pot_temp = vdwMult * (myPot - myPotC); |
| 219 |
< |
vpair += pot_temp; |
| 245 |
< |
|
| 246 |
< |
RealType dudr = sw * vdwMult * (myDeriv - myDerivC); |
| 218 |
> |
RealType pot_temp = *(idat.vdwMult) * (myPot - myPotC); |
| 219 |
> |
*(idat.vpair) += pot_temp; |
| 220 |
|
|
| 221 |
< |
pot += sw * pot_temp; |
| 249 |
< |
f1 = d * dudr / r; |
| 221 |
> |
RealType dudr = *(idat.sw) * *(idat.vdwMult) * (myDeriv - myDerivC); |
| 222 |
|
|
| 251 |
– |
return; |
| 252 |
– |
|
| 253 |
– |
} |
| 254 |
– |
|
| 255 |
– |
void Morse::do_morse_pair(int *atid1, int *atid2, RealType *d, |
| 256 |
– |
RealType *rij, RealType *r2, RealType *rcut, |
| 257 |
– |
RealType *sw, RealType *vdwMult, |
| 258 |
– |
RealType *vpair, RealType *pot, RealType *f1) { |
| 259 |
– |
|
| 260 |
– |
if (!initialized_) initialize(); |
| 223 |
|
|
| 224 |
< |
AtomType* atype1 = MorseMap[*atid1]; |
| 225 |
< |
AtomType* atype2 = MorseMap[*atid2]; |
| 224 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
| 225 |
> |
*(idat.f1) = *(idat.d) * dudr / *(idat.rij); |
| 226 |
|
|
| 265 |
– |
Vector3d disp(d[0], d[1], d[2]); |
| 266 |
– |
Vector3d frc(f1[0], f1[1], f1[2]); |
| 267 |
– |
|
| 268 |
– |
calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, |
| 269 |
– |
*pot, frc); |
| 270 |
– |
|
| 271 |
– |
f1[0] = frc.x(); |
| 272 |
– |
f1[1] = frc.y(); |
| 273 |
– |
f1[2] = frc.z(); |
| 274 |
– |
|
| 227 |
|
return; |
| 228 |
|
} |
| 277 |
– |
|
| 278 |
– |
void Morse::setMorseDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { |
| 279 |
– |
shiftedPot_ = (bool)(*sP); |
| 280 |
– |
shiftedFrc_ = (bool)(*sF); |
| 281 |
– |
} |
| 282 |
– |
} |
| 229 |
|
|
| 230 |
< |
extern "C" { |
| 231 |
< |
|
| 286 |
< |
#define fortranSetMorseCutoff FC_FUNC(setmorsedefaultcutoff, SETMORSEDEFAULTCUTOFF) |
| 287 |
< |
#define fortranDoMorsePair FC_FUNC(do_morse_pair, DO_MORSE_PAIR) |
| 288 |
< |
|
| 289 |
< |
void fortranSetMorseCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { |
| 290 |
< |
return OpenMD::Morse::Instance()->setMorseDefaultCutoff(rcut, shiftedPot, |
| 291 |
< |
shiftedFrc); |
| 292 |
< |
} |
| 293 |
< |
void fortranDoMorsePair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 294 |
< |
RealType *r2, RealType *rcut, RealType *sw, |
| 295 |
< |
RealType *vdwMult, RealType* vpair, RealType* pot, |
| 296 |
< |
RealType *f1){ |
| 230 |
> |
RealType Morse::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 231 |
> |
if (!initialized_) initialize(); |
| 232 |
|
|
| 233 |
< |
return OpenMD::Morse::Instance()->do_morse_pair(atid1, atid2, d, rij, r2, |
| 234 |
< |
rcut, sw, vdwMult, vpair, |
| 235 |
< |
pot, f1); |
| 233 |
> |
int atid1 = atypes.first->getIdent(); |
| 234 |
> |
int atid2 = atypes.second->getIdent(); |
| 235 |
> |
int mtid1 = Mtids[atid1]; |
| 236 |
> |
int mtid2 = Mtids[atid2]; |
| 237 |
> |
|
| 238 |
> |
if ( mtid1 == -1 || mtid2 == -1) return 0.0; |
| 239 |
> |
else { |
| 240 |
> |
MorseInteractionData mixer = MixingMap[mtid1][mtid2]; |
| 241 |
> |
RealType Re = mixer.Re; |
| 242 |
> |
RealType beta = mixer.beta; |
| 243 |
> |
// This value of the r corresponds to an energy about 1.48% of |
| 244 |
> |
// the energy at the bottom of the Morse well. For comparison, the |
| 245 |
> |
// Lennard-Jones function is about 1.63% of it's minimum value at |
| 246 |
> |
// a distance of 2.5 sigma. |
| 247 |
> |
return (4.9 + beta * Re) / beta; |
| 248 |
> |
} |
| 249 |
|
} |
| 250 |
|
} |
| 251 |
+ |
|
