| 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> |
| 45 |
|
|
| 46 |
|
#include <cmath> |
| 47 |
|
#include "nonbonded/GB.hpp" |
| 47 |
– |
#include "nonbonded/LJ.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
+ |
#include "types/LennardJonesAdapter.hpp" |
| 50 |
+ |
#include "types/GayBerneAdapter.hpp" |
| 51 |
|
|
| 52 |
|
using namespace std; |
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 55 |
< |
bool GB::initialized_ = false; |
| 56 |
< |
RealType GB::mu_ = 2.0; |
| 57 |
< |
RealType GB::nu_ = 1.0; |
| 58 |
< |
ForceField* GB::forceField_ = NULL; |
| 59 |
< |
map<int, AtomType*> GB::GBMap; |
| 60 |
< |
map<pair<AtomType*, AtomType*>, GBInteractionData> GB::MixingMap; |
| 61 |
< |
|
| 62 |
< |
GB* GB::_instance = NULL; |
| 55 |
> |
/* GB is the Gay-Berne interaction for ellipsoidal particles. The original |
| 56 |
> |
* paper (for identical uniaxial particles) is: |
| 57 |
> |
* J. G. Gay and B. J. Berne, J. Chem. Phys., 74, 3316-3319 (1981). |
| 58 |
> |
* A more-general GB potential for dissimilar uniaxial particles: |
| 59 |
> |
* D. J. Cleaver, C. M. Care, M. P. Allen and M. P. Neal, Phys. Rev. E, |
| 60 |
> |
* 54, 559-567 (1996). |
| 61 |
> |
* Further parameterizations can be found in: |
| 62 |
> |
* A. P. J. Emerson, G. R. Luckhurst and S. G. Whatling, Mol. Phys., |
| 63 |
> |
* 82, 113-124 (1994). |
| 64 |
> |
* And a nice force expression: |
| 65 |
> |
* G. R. Luckhurst and R. A. Stephens, Liq. Cryst. 8, 451-464 (1990). |
| 66 |
> |
* Even clearer force and torque expressions: |
| 67 |
> |
* P. A. Golubkov and P. Y. Ren, J. Chem. Phys., 125, 64103 (2006). |
| 68 |
> |
* New expressions for cross interactions of strength parameters: |
| 69 |
> |
* J. Wu, X. Zhen, H. Shen, G. Li, and P. Ren, J. Chem. Phys., |
| 70 |
> |
* 135, 155104 (2011). |
| 71 |
> |
* |
| 72 |
> |
* In this version of the GB interaction, each uniaxial ellipsoidal type |
| 73 |
> |
* is described using a set of 6 parameters: |
| 74 |
> |
* d: range parameter for side-by-side (S) and cross (X) configurations |
| 75 |
> |
* l: range parameter for end-to-end (E) configuration |
| 76 |
> |
* epsilon_X: well-depth parameter for cross (X) configuration |
| 77 |
> |
* epsilon_S: well-depth parameter for side-by-side (S) configuration |
| 78 |
> |
* epsilon_E: well depth parameter for end-to-end (E) configuration |
| 79 |
> |
* dw: "softness" of the potential |
| 80 |
> |
* |
| 81 |
> |
* Additionally, there are two "universal" paramters to govern the overall |
| 82 |
> |
* importance of the purely orientational (nu) and the mixed |
| 83 |
> |
* orientational / translational (mu) parts of strength of the interactions. |
| 84 |
> |
* These parameters have default or "canonical" values, but may be changed |
| 85 |
> |
* as a force field option: |
| 86 |
> |
* nu_: purely orientational part : defaults to 1 |
| 87 |
> |
* mu_: mixed orientational / translational part : defaults to 2 |
| 88 |
> |
*/ |
| 89 |
|
|
| 62 |
– |
GB* GB::Instance() { |
| 63 |
– |
if (!_instance) { |
| 64 |
– |
_instance = new GB(); |
| 65 |
– |
} |
| 66 |
– |
return _instance; |
| 67 |
– |
} |
| 90 |
|
|
| 91 |
< |
GayBerneParam GB::getGayBerneParam(AtomType* atomType) { |
| 91 |
> |
GB::GB() : initialized_(false), name_("GB"), forceField_(NULL), |
| 92 |
> |
mu_(2.0), nu_(1.0) {} |
| 93 |
|
|
| 94 |
< |
// Do sanity checking on the AtomType we were passed before |
| 72 |
< |
// building any data structures: |
| 73 |
< |
if (!atomType->isGayBerne()) { |
| 74 |
< |
sprintf( painCave.errMsg, |
| 75 |
< |
"GB::getGayBerneParam was passed an atomType (%s) that does\n" |
| 76 |
< |
"\tnot appear to be a Gay-Berne atom.\n", |
| 77 |
< |
atomType->getName().c_str()); |
| 78 |
< |
painCave.severity = OPENMD_ERROR; |
| 79 |
< |
painCave.isFatal = 1; |
| 80 |
< |
simError(); |
| 81 |
< |
} |
| 94 |
> |
void GB::initialize() { |
| 95 |
|
|
| 96 |
< |
DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 97 |
< |
GenericData* data = daType->getPropertyByName("GayBerne"); |
| 98 |
< |
if (data == NULL) { |
| 99 |
< |
sprintf( painCave.errMsg, "GB::getGayBerneParam could not find\n" |
| 87 |
< |
"\tGay-Berne parameters for atomType %s.\n", |
| 88 |
< |
daType->getName().c_str()); |
| 89 |
< |
painCave.severity = OPENMD_ERROR; |
| 90 |
< |
painCave.isFatal = 1; |
| 91 |
< |
simError(); |
| 92 |
< |
} |
| 93 |
< |
|
| 94 |
< |
GayBerneParamGenericData* gbData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 95 |
< |
if (gbData == NULL) { |
| 96 |
< |
sprintf( painCave.errMsg, |
| 97 |
< |
"GB::getGayBerneParam could not convert GenericData to\n" |
| 98 |
< |
"\tGayBerneParamGenericData for atom type %s\n", |
| 99 |
< |
daType->getName().c_str()); |
| 100 |
< |
painCave.severity = OPENMD_ERROR; |
| 101 |
< |
painCave.isFatal = 1; |
| 102 |
< |
simError(); |
| 103 |
< |
} |
| 104 |
< |
|
| 105 |
< |
return gbData->getData(); |
| 106 |
< |
} |
| 96 |
> |
GBtypes.clear(); |
| 97 |
> |
GBtids.clear(); |
| 98 |
> |
MixingMap.clear(); |
| 99 |
> |
nGB_ = 0; |
| 100 |
|
|
| 101 |
< |
void GB::initialize() { |
| 109 |
< |
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 110 |
< |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 111 |
< |
AtomType* at; |
| 101 |
> |
GBtids.resize( forceField_->getNAtomType(), -1); |
| 102 |
|
|
| 103 |
+ |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 104 |
+ |
mu_ = fopts.getGayBerneMu(); |
| 105 |
+ |
nu_ = fopts.getGayBerneNu(); |
| 106 |
+ |
|
| 107 |
|
// GB handles all of the GB-GB interactions as well as GB-LJ cross |
| 108 |
|
// interactions: |
| 109 |
+ |
set<AtomType*>::iterator at; |
| 110 |
+ |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 111 |
+ |
if ((*at)->isGayBerne()) nGB_++; |
| 112 |
+ |
if ((*at)->isLennardJones()) nGB_++; |
| 113 |
+ |
} |
| 114 |
|
|
| 115 |
< |
for (at = atomTypes->beginType(i); at != NULL; |
| 116 |
< |
at = atomTypes->nextType(i)) { |
| 117 |
< |
|
| 119 |
< |
if (at->isGayBerne() || at->isLennardJones()) |
| 120 |
< |
addType(at); |
| 115 |
> |
MixingMap.resize(nGB_); |
| 116 |
> |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 117 |
> |
if ((*at)->isGayBerne() || (*at)->isLennardJones()) addType( *at ); |
| 118 |
|
} |
| 119 |
< |
|
| 119 |
> |
|
| 120 |
|
initialized_ = true; |
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
void GB::addType(AtomType* atomType){ |
| 127 |
– |
// add it to the map: |
| 128 |
– |
AtomTypeProperties atp = atomType->getATP(); |
| 124 |
|
|
| 125 |
< |
pair<map<int,AtomType*>::iterator,bool> ret; |
| 126 |
< |
ret = GBMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
| 125 |
> |
// add it to the map: |
| 126 |
> |
int atid = atomType->getIdent(); |
| 127 |
> |
int gbtid = GBtypes.size(); |
| 128 |
> |
|
| 129 |
> |
pair<set<int>::iterator,bool> ret; |
| 130 |
> |
ret = GBtypes.insert( atid ); |
| 131 |
|
if (ret.second == false) { |
| 132 |
|
sprintf( painCave.errMsg, |
| 133 |
|
"GB already had a previous entry with ident %d\n", |
| 134 |
< |
atp.ident); |
| 134 |
> |
atid) ; |
| 135 |
|
painCave.severity = OPENMD_INFO; |
| 136 |
|
painCave.isFatal = 0; |
| 137 |
|
simError(); |
| 138 |
|
} |
| 139 |
+ |
|
| 140 |
+ |
GBtids[atid] = gbtid; |
| 141 |
+ |
MixingMap[gbtid].resize( nGB_ ); |
| 142 |
|
|
| 143 |
< |
RealType d1, l1, e1, er1, dw1; |
| 143 |
> |
RealType d1(0.0), l1(0.0), eX1(0.0), eS1(0.0), eE1(0.0), dw1(0.0); |
| 144 |
|
|
| 145 |
< |
if (atomType->isGayBerne()) { |
| 146 |
< |
GayBerneParam gb1 = getGayBerneParam(atomType); |
| 147 |
< |
d1 = gb1.GB_d; |
| 148 |
< |
l1 = gb1.GB_l; |
| 149 |
< |
e1 = gb1.GB_eps; |
| 150 |
< |
er1 = gb1.GB_eps_ratio; |
| 151 |
< |
dw1 = gb1.GB_dw; |
| 152 |
< |
} else if (atomType->isLennardJones()) { |
| 153 |
< |
d1 = LJ::Instance()->getSigma(atomType) / sqrt(2.0); |
| 154 |
< |
e1 = LJ::Instance()->getEpsilon(atomType); |
| 145 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
| 146 |
> |
GayBerneAdapter gba1 = GayBerneAdapter(atomType); |
| 147 |
> |
if (gba1.isGayBerne()) { |
| 148 |
> |
d1 = gba1.getD(); |
| 149 |
> |
l1 = gba1.getL(); |
| 150 |
> |
eX1 = gba1.getEpsX(); |
| 151 |
> |
eS1 = gba1.getEpsS(); |
| 152 |
> |
eE1 = gba1.getEpsE(); |
| 153 |
> |
dw1 = gba1.getDw(); |
| 154 |
> |
} else if (lja1.isLennardJones()) { |
| 155 |
> |
d1 = lja1.getSigma() / sqrt(2.0); |
| 156 |
|
l1 = d1; |
| 157 |
< |
er1 = 1.0; |
| 157 |
> |
eX1 = lja1.getEpsilon(); |
| 158 |
> |
eS1 = eX1; |
| 159 |
> |
eE1 = eX1; |
| 160 |
|
dw1 = 1.0; |
| 161 |
|
} else { |
| 162 |
|
sprintf( painCave.errMsg, |
| 168 |
|
simError(); |
| 169 |
|
} |
| 170 |
|
|
| 171 |
< |
|
| 171 |
> |
|
| 172 |
|
// Now, iterate over all known types and add to the mixing map: |
| 173 |
|
|
| 174 |
< |
map<int, AtomType*>::iterator it; |
| 175 |
< |
for( it = GBMap.begin(); it != GBMap.end(); ++it) { |
| 174 |
> |
std::set<int>::iterator it; |
| 175 |
> |
for( it = GBtypes.begin(); it != GBtypes.end(); ++it) { |
| 176 |
|
|
| 177 |
< |
AtomType* atype2 = (*it).second; |
| 177 |
> |
int gbtid2 = GBtids[ (*it) ]; |
| 178 |
> |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 179 |
> |
|
| 180 |
> |
LennardJonesAdapter lja2 = LennardJonesAdapter(atype2); |
| 181 |
> |
GayBerneAdapter gba2 = GayBerneAdapter(atype2); |
| 182 |
> |
RealType d2(0.0), l2(0.0), eX2(0.0), eS2(0.0), eE2(0.0), dw2(0.0); |
| 183 |
|
|
| 184 |
< |
RealType d2, l2, e2, er2, dw2; |
| 185 |
< |
|
| 186 |
< |
if (atype2->isGayBerne()) { |
| 187 |
< |
GayBerneParam gb2 = getGayBerneParam(atype2); |
| 188 |
< |
d2 = gb2.GB_d; |
| 189 |
< |
l2 = gb2.GB_l; |
| 190 |
< |
e2 = gb2.GB_eps; |
| 191 |
< |
er2 = gb2.GB_eps_ratio; |
| 192 |
< |
dw2 = gb2.GB_dw; |
| 183 |
< |
} else if (atype2->isLennardJones()) { |
| 184 |
< |
d2 = LJ::Instance()->getSigma(atype2) / sqrt(2.0); |
| 185 |
< |
e2 = LJ::Instance()->getEpsilon(atype2); |
| 184 |
> |
if (gba2.isGayBerne()) { |
| 185 |
> |
d2 = gba2.getD(); |
| 186 |
> |
l2 = gba2.getL(); |
| 187 |
> |
eX2 = gba2.getEpsX(); |
| 188 |
> |
eS2 = gba2.getEpsS(); |
| 189 |
> |
eE2 = gba2.getEpsE(); |
| 190 |
> |
dw2 = gba2.getDw(); |
| 191 |
> |
} else if (lja2.isLennardJones()) { |
| 192 |
> |
d2 = lja2.getSigma() / sqrt(2.0); |
| 193 |
|
l2 = d2; |
| 194 |
< |
er2 = 1.0; |
| 194 |
> |
eX2 = lja2.getEpsilon(); |
| 195 |
> |
eS2 = eX2; |
| 196 |
> |
eE2 = eX2; |
| 197 |
|
dw2 = 1.0; |
| 198 |
< |
} |
| 199 |
< |
|
| 200 |
< |
GBInteractionData mixer; |
| 198 |
> |
} else { |
| 199 |
> |
sprintf( painCave.errMsg, |
| 200 |
> |
"GB::addType found an atomType (%s) that does not\n" |
| 201 |
> |
"\tappear to be a Gay-Berne or Lennard-Jones atom.\n", |
| 202 |
> |
atype2->getName().c_str()); |
| 203 |
> |
painCave.severity = OPENMD_ERROR; |
| 204 |
> |
painCave.isFatal = 1; |
| 205 |
> |
simError(); |
| 206 |
> |
} |
| 207 |
|
|
| 208 |
+ |
|
| 209 |
+ |
GBInteractionData mixer1, mixer2; |
| 210 |
+ |
|
| 211 |
|
// Cleaver paper uses sqrt of squares to get sigma0 for |
| 212 |
|
// mixed interactions. |
| 213 |
< |
|
| 214 |
< |
mixer.sigma0 = sqrt(d1*d1 + d2*d2); |
| 215 |
< |
mixer.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
| 216 |
< |
mixer.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
| 217 |
< |
mixer.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
| 213 |
> |
|
| 214 |
> |
mixer1.sigma0 = sqrt(d1*d1 + d2*d2); |
| 215 |
> |
mixer1.xa2 = (l1*l1 - d1*d1)/(l1*l1 + d2*d2); |
| 216 |
> |
mixer1.xai2 = (l2*l2 - d2*d2)/(l2*l2 + d1*d1); |
| 217 |
> |
mixer1.x2 = (l1*l1 - d1*d1) * (l2*l2 - d2*d2) / |
| 218 |
|
((l2*l2 + d1*d1) * (l1*l1 + d2*d2)); |
| 201 |
– |
|
| 202 |
– |
// assumed LB mixing rules for now: |
| 203 |
– |
|
| 204 |
– |
mixer.dw = 0.5 * (dw1 + dw2); |
| 205 |
– |
mixer.eps0 = sqrt(e1 * e2); |
| 219 |
|
|
| 220 |
< |
RealType er = sqrt(er1 * er2); |
| 221 |
< |
RealType ermu = pow(er,(1.0 / mu_)); |
| 222 |
< |
RealType xp = (1.0 - ermu) / (1.0 + ermu); |
| 223 |
< |
RealType ap2 = 1.0 / (1.0 + ermu); |
| 220 |
> |
mixer2.sigma0 = mixer1.sigma0; |
| 221 |
> |
// xa2 and xai2 for j-i pairs are reversed from the same i-j pairing. |
| 222 |
> |
// Swapping the particles reverses the anisotropy parameters: |
| 223 |
> |
mixer2.xa2 = mixer1.xai2; |
| 224 |
> |
mixer2.xai2 = mixer1.xa2; |
| 225 |
> |
mixer2.x2 = mixer1.x2; |
| 226 |
|
|
| 227 |
< |
mixer.xp2 = xp * xp; |
| 228 |
< |
mixer.xpap2 = xp * ap2; |
| 229 |
< |
mixer.xpapi2 = xp / ap2; |
| 227 |
> |
// assumed LB mixing rules for now: |
| 228 |
> |
|
| 229 |
> |
mixer1.dw = 0.5 * (dw1 + dw2); |
| 230 |
> |
mixer1.eps0 = sqrt(eX1 * eX2); |
| 231 |
|
|
| 232 |
< |
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 232 |
> |
mixer2.dw = mixer1.dw; |
| 233 |
> |
mixer2.eps0 = mixer1.eps0; |
| 234 |
> |
|
| 235 |
> |
RealType mi = RealType(1.0)/mu_; |
| 236 |
> |
|
| 237 |
> |
mixer1.xpap2 = (pow(eS1, mi) - pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)); |
| 238 |
> |
mixer1.xpapi2 = (pow(eS2, mi) - pow(eE2, mi)) / (pow(eS2, mi) + pow(eE1, mi)); |
| 239 |
> |
mixer1.xp2 = (pow(eS1, mi) - pow(eE1, mi)) * (pow(eS2, mi) - pow(eE2, mi)) / |
| 240 |
> |
(pow(eS2, mi) + pow(eE1, mi)) / (pow(eS1, mi) + pow(eE2, mi)) ; |
| 241 |
> |
|
| 242 |
> |
// xpap2 and xpapi2 for j-i pairs are reversed from the same i-j pairing. |
| 243 |
> |
// Swapping the particles reverses the anisotropy parameters: |
| 244 |
> |
mixer2.xpap2 = mixer1.xpapi2; |
| 245 |
> |
mixer2.xpapi2 = mixer1.xpap2; |
| 246 |
> |
mixer2.xp2 = mixer1.xp2; |
| 247 |
> |
// keep track of who is the LJ atom: |
| 248 |
> |
mixer1.i_is_LJ = atomType->isLennardJones(); |
| 249 |
> |
mixer1.j_is_LJ = atype2->isLennardJones(); |
| 250 |
> |
mixer2.i_is_LJ = mixer1.j_is_LJ; |
| 251 |
> |
mixer2.j_is_LJ = mixer1.i_is_LJ; |
| 252 |
|
|
| 218 |
– |
if (atomType->isGayBerne() || atype2->isGayBerne()) { |
| 253 |
|
|
| 254 |
< |
pair<AtomType*, AtomType*> key1, key2; |
| 221 |
< |
key1 = make_pair(atomType, atype2); |
| 222 |
< |
key2 = make_pair(atype2, atomType); |
| 223 |
< |
|
| 224 |
< |
MixingMap[key1] = mixer; |
| 225 |
< |
if (key2 != key1) { |
| 226 |
< |
MixingMap[key2] = mixer; |
| 227 |
< |
} |
| 228 |
< |
} |
| 229 |
< |
} |
| 230 |
< |
} |
| 231 |
< |
|
| 254 |
> |
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 255 |
|
|
| 256 |
< |
RealType GB::getGayBerneCut(int atid) { |
| 257 |
< |
if (!initialized_) initialize(); |
| 258 |
< |
std::map<int, AtomType*> :: const_iterator it; |
| 259 |
< |
it = GBMap.find(atid); |
| 260 |
< |
if (it == GBMap.end()) { |
| 261 |
< |
sprintf( painCave.errMsg, |
| 262 |
< |
"GB::getGayBerneCut could not find atid %d in GBMap\n", |
| 240 |
< |
(atid)); |
| 241 |
< |
painCave.severity = OPENMD_ERROR; |
| 242 |
< |
painCave.isFatal = 1; |
| 243 |
< |
simError(); |
| 256 |
> |
if (gba1.isGayBerne() || gba2.isGayBerne()) { |
| 257 |
> |
MixingMap[gbtid2].resize( nGB_ ); |
| 258 |
> |
MixingMap[gbtid][gbtid2] = mixer1; |
| 259 |
> |
if (gbtid2 != gbtid) { |
| 260 |
> |
MixingMap[gbtid2][gbtid] = mixer2; |
| 261 |
> |
} |
| 262 |
> |
} |
| 263 |
|
} |
| 245 |
– |
|
| 246 |
– |
AtomType* atype = it->second; |
| 247 |
– |
|
| 248 |
– |
RealType gbCut; |
| 249 |
– |
|
| 250 |
– |
if (atype->isGayBerne()) { |
| 251 |
– |
GayBerneParam gb = getGayBerneParam(atype); |
| 252 |
– |
|
| 253 |
– |
// sigma is actually sqrt(2) * l for prolate ellipsoids |
| 254 |
– |
gbCut = 2.5 * sqrt(2.0) * max(gb.GB_l, gb.GB_d); |
| 255 |
– |
|
| 256 |
– |
} else if (atype->isLennardJones()) { |
| 257 |
– |
gbCut = 2.5 * LJ::Instance()->getSigma(atype); |
| 258 |
– |
} |
| 259 |
– |
|
| 260 |
– |
return gbCut; |
| 264 |
|
} |
| 265 |
+ |
|
| 266 |
+ |
void GB::calcForce(InteractionData &idat) { |
| 267 |
|
|
| 263 |
– |
|
| 264 |
– |
void GB::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 265 |
– |
RealType r, RealType r2, RealType sw, |
| 266 |
– |
RealType vdwMult, RealType &vpair, RealType &pot, |
| 267 |
– |
RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
| 268 |
– |
Vector3d &t1, Vector3d &t2) { |
| 269 |
– |
|
| 268 |
|
if (!initialized_) initialize(); |
| 269 |
|
|
| 270 |
< |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 273 |
< |
GBInteractionData mixer = MixingMap[key]; |
| 270 |
> |
GBInteractionData &mixer = MixingMap[GBtids[idat.atid1]][GBtids[idat.atid2]]; |
| 271 |
|
|
| 272 |
|
RealType sigma0 = mixer.sigma0; |
| 273 |
|
RealType dw = mixer.dw; |
| 279 |
|
RealType xpap2 = mixer.xpap2; |
| 280 |
|
RealType xpapi2 = mixer.xpapi2; |
| 281 |
|
|
| 282 |
< |
Vector3d ul1 = A1.getColumn(2); |
| 283 |
< |
Vector3d ul2 = A2.getColumn(2); |
| 282 |
> |
Vector3d ul1 = idat.A1->getRow(2); |
| 283 |
> |
Vector3d ul2 = idat.A2->getRow(2); |
| 284 |
|
|
| 285 |
|
RealType a, b, g; |
| 286 |
< |
|
| 287 |
< |
bool i_is_LJ = at1->isLennardJones(); |
| 291 |
< |
bool j_is_LJ = at2->isLennardJones(); |
| 292 |
< |
|
| 293 |
< |
if (i_is_LJ) { |
| 286 |
> |
|
| 287 |
> |
if (mixer.i_is_LJ) { |
| 288 |
|
a = 0.0; |
| 289 |
|
ul1 = V3Zero; |
| 290 |
|
} else { |
| 291 |
< |
a = dot(d, ul1); |
| 291 |
> |
a = dot(*(idat.d), ul1); |
| 292 |
|
} |
| 293 |
|
|
| 294 |
< |
if (j_is_LJ) { |
| 294 |
> |
if (mixer.j_is_LJ) { |
| 295 |
|
b = 0.0; |
| 296 |
|
ul2 = V3Zero; |
| 297 |
|
} else { |
| 298 |
< |
b = dot(d, ul2); |
| 298 |
> |
b = dot(*(idat.d), ul2); |
| 299 |
|
} |
| 300 |
|
|
| 301 |
< |
if (i_is_LJ || j_is_LJ) |
| 301 |
> |
if (mixer.i_is_LJ || mixer.j_is_LJ) |
| 302 |
|
g = 0.0; |
| 303 |
|
else |
| 304 |
|
g = dot(ul1, ul2); |
| 305 |
|
|
| 306 |
< |
RealType au = a / r; |
| 307 |
< |
RealType bu = b / r; |
| 306 |
> |
RealType au = a / *(idat.rij); |
| 307 |
> |
RealType bu = b / *(idat.rij); |
| 308 |
|
|
| 309 |
|
RealType au2 = au * au; |
| 310 |
|
RealType bu2 = bu * bu; |
| 311 |
|
RealType g2 = g * g; |
| 312 |
< |
|
| 312 |
> |
|
| 313 |
|
RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
| 314 |
|
RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
| 315 |
|
|
| 317 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 318 |
|
RealType e2 = 1.0 - Hp; |
| 319 |
|
RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
| 320 |
< |
RealType BigR = dw*sigma0 / (r - sigma + dw*sigma0); |
| 320 |
> |
RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0); |
| 321 |
|
|
| 322 |
|
RealType R3 = BigR*BigR*BigR; |
| 323 |
|
RealType R6 = R3*R3; |
| 325 |
|
RealType R12 = R6*R6; |
| 326 |
|
RealType R13 = R6*R7; |
| 327 |
|
|
| 328 |
< |
RealType U = vdwMult * 4.0 * eps * (R12 - R6); |
| 328 |
> |
RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6); |
| 329 |
|
|
| 330 |
|
RealType s3 = sigma*sigma*sigma; |
| 331 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 332 |
|
|
| 333 |
< |
RealType pref1 = - vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * r); |
| 333 |
> |
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 334 |
> |
(e2 * *(idat.rij)); |
| 335 |
|
|
| 336 |
< |
RealType pref2 = vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*r*s03); |
| 336 |
> |
RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) / |
| 337 |
> |
(dw* *(idat.rij) * s03); |
| 338 |
|
|
| 339 |
< |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 + H)); |
| 339 |
> |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 * |
| 340 |
> |
*(idat.rij) / s3 + H)); |
| 341 |
|
|
| 342 |
|
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 343 |
|
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 344 |
|
|
| 345 |
|
RealType dUdb = pref1 * (xpapi2*bu - xp2*au*g) / (1.0 - xp2 * g2) |
| 346 |
|
+ pref2 * (xai2 * bu - x2 *au*g) / (1.0 - x2 * g2); |
| 347 |
< |
|
| 347 |
> |
|
| 348 |
|
RealType dUdg = 4.0 * eps * nu_ * (R12 - R6) * x2 * g / (1.0 - x2*g2) |
| 349 |
|
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 350 |
|
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 351 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 352 |
|
|
| 353 |
< |
|
| 354 |
< |
Vector3d rhat = d / r; |
| 355 |
< |
Vector3d rxu1 = cross(d, ul1); |
| 359 |
< |
Vector3d rxu2 = cross(d, ul2); |
| 353 |
> |
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 354 |
> |
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 355 |
> |
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 356 |
|
Vector3d uxu = cross(ul1, ul2); |
| 357 |
|
|
| 358 |
< |
pot += U*sw; |
| 359 |
< |
f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 360 |
< |
t1 += dUda * rxu1 - dUdg * uxu; |
| 361 |
< |
t2 += dUdb * rxu2 - dUdg * uxu; |
| 362 |
< |
vpair += U*sw; |
| 358 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 359 |
> |
*(idat.f1) += (dUdr * rhat + dUda * ul1 + dUdb * ul2) * *(idat.sw); |
| 360 |
> |
*(idat.t1) += (dUda * rxu1 - dUdg * uxu) * *(idat.sw); |
| 361 |
> |
*(idat.t2) += (dUdb * rxu2 + dUdg * uxu) * *(idat.sw); |
| 362 |
> |
*(idat.vpair) += U; |
| 363 |
|
|
| 364 |
|
return; |
| 365 |
|
|
| 366 |
|
} |
| 367 |
|
|
| 368 |
< |
void GB::do_gb_pair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 369 |
< |
RealType *r2, RealType *sw, RealType *vdwMult, |
| 374 |
< |
RealType *vpair, RealType *pot, RealType *A1, |
| 375 |
< |
RealType *A2, RealType *f1, RealType *t1, RealType *t2) { |
| 376 |
< |
|
| 377 |
< |
if (!initialized_) initialize(); |
| 378 |
< |
|
| 379 |
< |
AtomType* atype1 = GBMap[*atid1]; |
| 380 |
< |
AtomType* atype2 = GBMap[*atid2]; |
| 381 |
< |
|
| 382 |
< |
Vector3d disp(d); |
| 383 |
< |
Vector3d frc(f1); |
| 384 |
< |
Vector3d trq1(t1); |
| 385 |
< |
Vector3d trq2(t2); |
| 386 |
< |
RotMat3x3d Ai(A1); |
| 387 |
< |
RotMat3x3d Aj(A2); |
| 388 |
< |
|
| 389 |
< |
// Fortran has the opposite matrix ordering from c++, so we'll use |
| 390 |
< |
// transpose here. When we finish the conversion to C++, this wrapper |
| 391 |
< |
// will disappear, as will the transpose below: |
| 368 |
> |
RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 369 |
> |
if (!initialized_) initialize(); |
| 370 |
|
|
| 371 |
< |
calcForce(atype1, atype2, disp, *r, *r2, *sw, *vdwMult, *vpair, *pot, |
| 394 |
< |
Ai.transpose(), Aj.transpose(), frc, trq1, trq1); |
| 395 |
< |
|
| 396 |
< |
f1[0] = frc.x(); |
| 397 |
< |
f1[1] = frc.y(); |
| 398 |
< |
f1[2] = frc.z(); |
| 371 |
> |
RealType cut = 0.0; |
| 372 |
|
|
| 373 |
< |
t1[0] = trq1.x(); |
| 374 |
< |
t1[1] = trq1.y(); |
| 375 |
< |
t1[2] = trq1.z(); |
| 373 |
> |
LennardJonesAdapter lja1 = LennardJonesAdapter(atypes.first); |
| 374 |
> |
GayBerneAdapter gba1 = GayBerneAdapter(atypes.first); |
| 375 |
> |
LennardJonesAdapter lja2 = LennardJonesAdapter(atypes.second); |
| 376 |
> |
GayBerneAdapter gba2 = GayBerneAdapter(atypes.second); |
| 377 |
|
|
| 378 |
< |
t2[0] = trq2.x(); |
| 379 |
< |
t2[1] = trq2.y(); |
| 380 |
< |
t2[2] = trq2.z(); |
| 378 |
> |
if (gba1.isGayBerne()) { |
| 379 |
> |
RealType d1 = gba1.getD(); |
| 380 |
> |
RealType l1 = gba1.getL(); |
| 381 |
> |
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 382 |
> |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
| 383 |
> |
} else if (lja1.isLennardJones()) { |
| 384 |
> |
cut = max(cut, RealType(2.5) * lja1.getSigma()); |
| 385 |
> |
} |
| 386 |
|
|
| 387 |
< |
return; |
| 387 |
> |
if (gba2.isGayBerne()) { |
| 388 |
> |
RealType d2 = gba2.getD(); |
| 389 |
> |
RealType l2 = gba2.getL(); |
| 390 |
> |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
| 391 |
> |
} else if (lja2.isLennardJones()) { |
| 392 |
> |
cut = max(cut, RealType(2.5) * lja2.getSigma()); |
| 393 |
> |
} |
| 394 |
> |
|
| 395 |
> |
return cut; |
| 396 |
|
} |
| 397 |
|
} |
| 398 |
|
|
| 412 |
– |
extern "C" { |
| 413 |
– |
|
| 414 |
– |
#define fortranGetGayBerneCut FC_FUNC(getgaybernecut, GETGAYBERNECUT) |
| 415 |
– |
#define fortranDoGBPair FC_FUNC(do_gb_pair, DO_GB_PAIR) |
| 416 |
– |
|
| 417 |
– |
RealType fortranGetGayBerneCut(int* atid) { |
| 418 |
– |
return OpenMD::GB::Instance()->getGayBerneCut(*atid); |
| 419 |
– |
} |
| 420 |
– |
|
| 421 |
– |
void fortranDoGBPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 422 |
– |
RealType *r2, RealType *sw, RealType *vdwMult, |
| 423 |
– |
RealType *vpair, RealType *pot, RealType *A1, |
| 424 |
– |
RealType *A2, RealType *f1, RealType *t1, RealType *t2){ |
| 425 |
– |
|
| 426 |
– |
return OpenMD::GB::Instance()->do_gb_pair(atid1, atid2, d, r, r2, sw, |
| 427 |
– |
vdwMult, vpair, pot, A1, A2, f1, |
| 428 |
– |
t1, t2); |
| 429 |
– |
} |
| 430 |
– |
} |
