| 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 |
|
|
| 43 |
|
#include <stdio.h> |
| 45 |
|
|
| 46 |
|
#include <cmath> |
| 47 |
|
#include "nonbonded/GB.hpp" |
| 47 |
– |
#include "nonbonded/LJ.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 50 |
|
using namespace std; |
| 51 |
|
namespace OpenMD { |
| 52 |
|
|
| 53 |
< |
bool GB::initialized_ = false; |
| 54 |
< |
RealType GB::mu_ = 2.0; |
| 55 |
< |
RealType GB::nu_ = 1.0; |
| 56 |
< |
ForceField* GB::forceField_ = NULL; |
| 57 |
< |
map<int, AtomType*> GB::GBMap; |
| 58 |
< |
map<pair<AtomType*, AtomType*>, GBInteractionData> GB::MixingMap; |
| 53 |
> |
GB::GB() : name_("GB"), initialized_(false), mu_(2.0), nu_(1.0), forceField_(NULL) {} |
| 54 |
|
|
| 60 |
– |
GB* GB::_instance = NULL; |
| 61 |
– |
|
| 62 |
– |
GB* GB::Instance() { |
| 63 |
– |
if (!_instance) { |
| 64 |
– |
_instance = new GB(); |
| 65 |
– |
} |
| 66 |
– |
return _instance; |
| 67 |
– |
} |
| 68 |
– |
|
| 55 |
|
GayBerneParam GB::getGayBerneParam(AtomType* atomType) { |
| 56 |
|
|
| 57 |
|
// Do sanity checking on the AtomType we were passed before |
| 91 |
|
return gbData->getData(); |
| 92 |
|
} |
| 93 |
|
|
| 94 |
+ |
LJParam GB::getLJParam(AtomType* atomType) { |
| 95 |
+ |
|
| 96 |
+ |
// Do sanity checking on the AtomType we were passed before |
| 97 |
+ |
// building any data structures: |
| 98 |
+ |
if (!atomType->isLennardJones()) { |
| 99 |
+ |
sprintf( painCave.errMsg, |
| 100 |
+ |
"GB::getLJParam was passed an atomType (%s) that does not\n" |
| 101 |
+ |
"\tappear to be a Lennard-Jones atom.\n", |
| 102 |
+ |
atomType->getName().c_str()); |
| 103 |
+ |
painCave.severity = OPENMD_ERROR; |
| 104 |
+ |
painCave.isFatal = 1; |
| 105 |
+ |
simError(); |
| 106 |
+ |
} |
| 107 |
+ |
|
| 108 |
+ |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 109 |
+ |
if (data == NULL) { |
| 110 |
+ |
sprintf( painCave.errMsg, "GB::getLJParam could not find Lennard-Jones\n" |
| 111 |
+ |
"\tparameters for atomType %s.\n", atomType->getName().c_str()); |
| 112 |
+ |
painCave.severity = OPENMD_ERROR; |
| 113 |
+ |
painCave.isFatal = 1; |
| 114 |
+ |
simError(); |
| 115 |
+ |
} |
| 116 |
+ |
|
| 117 |
+ |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 118 |
+ |
if (ljData == NULL) { |
| 119 |
+ |
sprintf( painCave.errMsg, |
| 120 |
+ |
"GB::getLJParam could not convert GenericData to LJParam for\n" |
| 121 |
+ |
"\tatom type %s\n", atomType->getName().c_str()); |
| 122 |
+ |
painCave.severity = OPENMD_ERROR; |
| 123 |
+ |
painCave.isFatal = 1; |
| 124 |
+ |
simError(); |
| 125 |
+ |
} |
| 126 |
+ |
|
| 127 |
+ |
return ljData->getData(); |
| 128 |
+ |
} |
| 129 |
+ |
|
| 130 |
+ |
RealType GB::getLJEpsilon(AtomType* atomType) { |
| 131 |
+ |
LJParam ljParam = getLJParam(atomType); |
| 132 |
+ |
return ljParam.epsilon; |
| 133 |
+ |
} |
| 134 |
+ |
RealType GB::getLJSigma(AtomType* atomType) { |
| 135 |
+ |
LJParam ljParam = getLJParam(atomType); |
| 136 |
+ |
return ljParam.sigma; |
| 137 |
+ |
} |
| 138 |
+ |
|
| 139 |
|
void GB::initialize() { |
| 140 |
+ |
|
| 141 |
+ |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 142 |
+ |
mu_ = fopts.getGayBerneMu(); |
| 143 |
+ |
nu_ = fopts.getGayBerneNu(); |
| 144 |
|
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 145 |
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 146 |
|
AtomType* at; |
| 183 |
|
er1 = gb1.GB_eps_ratio; |
| 184 |
|
dw1 = gb1.GB_dw; |
| 185 |
|
} else if (atomType->isLennardJones()) { |
| 186 |
< |
d1 = LJ::Instance()->getSigma(atomType) / sqrt(2.0); |
| 187 |
< |
e1 = LJ::Instance()->getEpsilon(atomType); |
| 186 |
> |
d1 = getLJSigma(atomType) / sqrt(2.0); |
| 187 |
> |
e1 = getLJEpsilon(atomType); |
| 188 |
|
l1 = d1; |
| 189 |
|
er1 = 1.0; |
| 190 |
|
dw1 = 1.0; |
| 216 |
|
er2 = gb2.GB_eps_ratio; |
| 217 |
|
dw2 = gb2.GB_dw; |
| 218 |
|
} else if (atype2->isLennardJones()) { |
| 219 |
< |
d2 = LJ::Instance()->getSigma(atype2) / sqrt(2.0); |
| 220 |
< |
e2 = LJ::Instance()->getEpsilon(atype2); |
| 219 |
> |
d2 = getLJSigma(atype2) / sqrt(2.0); |
| 220 |
> |
e2 = getLJEpsilon(atype2); |
| 221 |
|
l2 = d2; |
| 222 |
|
er2 = 1.0; |
| 223 |
|
dw2 = 1.0; |
| 240 |
|
mixer.eps0 = sqrt(e1 * e2); |
| 241 |
|
|
| 242 |
|
RealType er = sqrt(er1 * er2); |
| 243 |
< |
RealType ermu = pow(er,(1.0 / mu_)); |
| 243 |
> |
RealType ermu = pow(er, (RealType(1.0) / mu_)); |
| 244 |
|
RealType xp = (1.0 - ermu) / (1.0 + ermu); |
| 245 |
|
RealType ap2 = 1.0 / (1.0 + ermu); |
| 246 |
|
|
| 248 |
|
mixer.xpap2 = xp * ap2; |
| 249 |
|
mixer.xpapi2 = xp / ap2; |
| 250 |
|
|
| 251 |
+ |
cerr << "mixer" << er1 << " " << er2 << " " << mu_ << " " << ermu << " " << xp <<" " << ap2 << "\n"; |
| 252 |
+ |
|
| 253 |
|
// only add this pairing if at least one of the atoms is a Gay-Berne atom |
| 254 |
|
|
| 255 |
|
if (atomType->isGayBerne() || atype2->isGayBerne()) { |
| 265 |
|
} |
| 266 |
|
} |
| 267 |
|
} |
| 268 |
< |
|
| 268 |
> |
|
| 269 |
> |
void GB::calcForce(InteractionData &idat) { |
| 270 |
|
|
| 233 |
– |
RealType GB::getGayBerneCut(int atid) { |
| 271 |
|
if (!initialized_) initialize(); |
| 235 |
– |
std::map<int, AtomType*> :: const_iterator it; |
| 236 |
– |
it = GBMap.find(atid); |
| 237 |
– |
if (it == GBMap.end()) { |
| 238 |
– |
sprintf( painCave.errMsg, |
| 239 |
– |
"GB::getGayBerneCut could not find atid %d in GBMap\n", |
| 240 |
– |
(atid)); |
| 241 |
– |
painCave.severity = OPENMD_ERROR; |
| 242 |
– |
painCave.isFatal = 1; |
| 243 |
– |
simError(); |
| 244 |
– |
} |
| 245 |
– |
|
| 246 |
– |
AtomType* atype = it->second; |
| 247 |
– |
|
| 248 |
– |
RealType gbCut; |
| 272 |
|
|
| 273 |
< |
if (atype->isGayBerne()) { |
| 251 |
< |
GayBerneParam gb = getGayBerneParam(atype); |
| 273 |
> |
GBInteractionData mixer = MixingMap[idat.atypes]; |
| 274 |
|
|
| 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; |
| 261 |
– |
} |
| 262 |
– |
|
| 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 |
– |
|
| 270 |
– |
if (!initialized_) initialize(); |
| 271 |
– |
|
| 272 |
– |
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 273 |
– |
GBInteractionData mixer = MixingMap[key]; |
| 274 |
– |
|
| 275 |
|
RealType sigma0 = mixer.sigma0; |
| 276 |
|
RealType dw = mixer.dw; |
| 277 |
|
RealType eps0 = mixer.eps0; |
| 282 |
|
RealType xpap2 = mixer.xpap2; |
| 283 |
|
RealType xpapi2 = mixer.xpapi2; |
| 284 |
|
|
| 285 |
< |
Vector3d ul1 = A1.getColumn(2); |
| 286 |
< |
Vector3d ul2 = A2.getColumn(2); |
| 285 |
> |
Vector3d ul1 = idat.A1->getRow(2); |
| 286 |
> |
Vector3d ul2 = idat.A2->getRow(2); |
| 287 |
|
|
| 288 |
|
RealType a, b, g; |
| 289 |
|
|
| 290 |
< |
bool i_is_LJ = at1->isLennardJones(); |
| 291 |
< |
bool j_is_LJ = at2->isLennardJones(); |
| 292 |
< |
|
| 290 |
> |
bool i_is_LJ = idat.atypes.first->isLennardJones(); |
| 291 |
> |
bool j_is_LJ = idat.atypes.second->isLennardJones(); |
| 292 |
> |
|
| 293 |
|
if (i_is_LJ) { |
| 294 |
|
a = 0.0; |
| 295 |
|
ul1 = V3Zero; |
| 296 |
|
} else { |
| 297 |
< |
a = dot(d, ul1); |
| 297 |
> |
a = dot(*(idat.d), ul1); |
| 298 |
|
} |
| 299 |
|
|
| 300 |
|
if (j_is_LJ) { |
| 301 |
|
b = 0.0; |
| 302 |
|
ul2 = V3Zero; |
| 303 |
|
} else { |
| 304 |
< |
b = dot(d, ul2); |
| 304 |
> |
b = dot(*(idat.d), ul2); |
| 305 |
|
} |
| 306 |
|
|
| 307 |
|
if (i_is_LJ || j_is_LJ) |
| 309 |
|
else |
| 310 |
|
g = dot(ul1, ul2); |
| 311 |
|
|
| 312 |
< |
RealType au = a / r; |
| 313 |
< |
RealType bu = b / r; |
| 312 |
> |
cerr << "in GB, d = " << *(idat.d) << "\n"; |
| 313 |
> |
cerr << "abg = " << a << " " << b << " " << g <<"\n"; |
| 314 |
> |
|
| 315 |
> |
RealType au = a / *(idat.rij); |
| 316 |
> |
RealType bu = b / *(idat.rij); |
| 317 |
|
|
| 318 |
|
RealType au2 = au * au; |
| 319 |
|
RealType bu2 = bu * bu; |
| 321 |
|
|
| 322 |
|
RealType H = (xa2 * au2 + xai2 * bu2 - 2.0*x2*au*bu*g) / (1.0 - x2*g2); |
| 323 |
|
RealType Hp = (xpap2*au2 + xpapi2*bu2 - 2.0*xp2*au*bu*g) / (1.0 - xp2*g2); |
| 324 |
+ |
cerr << "xa2, xai2 " << xa2 << " " << xai2 << "\n"; |
| 325 |
+ |
cerr << "xpap2, xpapi2 " << xpap2 << " " << xpapi2 << "\n"; |
| 326 |
+ |
cerr << "H Hp = " << H << " " << Hp << "\n"; |
| 327 |
|
|
| 328 |
|
RealType sigma = sigma0 / sqrt(1.0 - H); |
| 329 |
|
RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
| 330 |
|
RealType e2 = 1.0 - Hp; |
| 331 |
|
RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
| 332 |
< |
RealType BigR = dw*sigma0 / (r - sigma + dw*sigma0); |
| 332 |
> |
cerr << "eps = " << eps0 << " " << e1 << " " << nu_ << " " << e2 << " " << mu_ << "\n"; |
| 333 |
> |
RealType BigR = dw*sigma0 / (*(idat.rij) - sigma + dw*sigma0); |
| 334 |
|
|
| 335 |
|
RealType R3 = BigR*BigR*BigR; |
| 336 |
|
RealType R6 = R3*R3; |
| 338 |
|
RealType R12 = R6*R6; |
| 339 |
|
RealType R13 = R6*R7; |
| 340 |
|
|
| 341 |
< |
RealType U = vdwMult * 4.0 * eps * (R12 - R6); |
| 341 |
> |
RealType U = *(idat.vdwMult) * 4.0 * eps * (R12 - R6); |
| 342 |
|
|
| 343 |
+ |
cerr << "R12, R6, eps = " << R12 << " " << R6 << " " << eps << " " << *(idat.vdwMult) << "\n"; |
| 344 |
+ |
|
| 345 |
|
RealType s3 = sigma*sigma*sigma; |
| 346 |
|
RealType s03 = sigma0*sigma0*sigma0; |
| 347 |
|
|
| 348 |
< |
RealType pref1 = - vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * r); |
| 348 |
> |
RealType pref1 = - *(idat.vdwMult) * 8.0 * eps * mu_ * (R12 - R6) / |
| 349 |
> |
(e2 * *(idat.rij)); |
| 350 |
|
|
| 351 |
< |
RealType pref2 = vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*r*s03); |
| 351 |
> |
RealType pref2 = *(idat.vdwMult) * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) / |
| 352 |
> |
(dw* *(idat.rij) * s03); |
| 353 |
|
|
| 354 |
< |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 + H)); |
| 354 |
> |
RealType dUdr = - (pref1 * Hp + pref2 * (sigma0 * sigma0 * |
| 355 |
> |
*(idat.rij) / s3 + H)); |
| 356 |
|
|
| 357 |
|
RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
| 358 |
|
+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
| 364 |
|
+ 8.0 * eps * mu_ * (R12 - R6) * (xp2*au*bu - Hp*xp2*g) / |
| 365 |
|
(1.0 - xp2 * g2) / e2 + 8.0 * eps * s3 * (3.0 * R7 - 6.0 * R13) * |
| 366 |
|
(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
| 355 |
– |
|
| 367 |
|
|
| 368 |
< |
Vector3d rhat = d / r; |
| 369 |
< |
Vector3d rxu1 = cross(d, ul1); |
| 370 |
< |
Vector3d rxu2 = cross(d, ul2); |
| 368 |
> |
cerr << pref1 << " " << pref2 << " " << dUdr <<" " << dUda << " " << dUdb << dUdg << "\n"; |
| 369 |
> |
|
| 370 |
> |
Vector3d rhat = *(idat.d) / *(idat.rij); |
| 371 |
> |
Vector3d rxu1 = cross(*(idat.d), ul1); |
| 372 |
> |
Vector3d rxu2 = cross(*(idat.d), ul2); |
| 373 |
|
Vector3d uxu = cross(ul1, ul2); |
| 374 |
+ |
|
| 375 |
+ |
cerr << "U = " << U << "\n"; |
| 376 |
+ |
cerr << "f1 = " << dUdr * rhat + dUda * ul1 + dUdb * ul2 << "\n"; |
| 377 |
+ |
cerr << "t1 = " << dUda * rxu1 - dUdg * uxu << "\n"; |
| 378 |
+ |
cerr << "t2 = " << dUdb * rxu2 - dUdg * uxu << "\n"; |
| 379 |
+ |
|
| 380 |
|
|
| 381 |
< |
pot += U*sw; |
| 382 |
< |
f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 383 |
< |
t1 += dUda * rxu1 - dUdg * uxu; |
| 384 |
< |
t2 += dUdb * rxu2 - dUdg * uxu; |
| 385 |
< |
vpair += U*sw; |
| 381 |
> |
(*(idat.pot))[VANDERWAALS_FAMILY] += U * *(idat.sw); |
| 382 |
> |
*(idat.f1) += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
| 383 |
> |
*(idat.t1) += dUda * rxu1 - dUdg * uxu; |
| 384 |
> |
*(idat.t2) += dUdb * rxu2 - dUdg * uxu; |
| 385 |
> |
*(idat.vpair) += U * *(idat.sw); |
| 386 |
|
|
| 387 |
|
return; |
| 388 |
|
|
| 389 |
|
} |
| 390 |
|
|
| 391 |
< |
void GB::do_gb_pair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 392 |
< |
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: |
| 391 |
> |
RealType GB::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 392 |
> |
if (!initialized_) initialize(); |
| 393 |
|
|
| 394 |
< |
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(); |
| 394 |
> |
RealType cut = 0.0; |
| 395 |
|
|
| 396 |
< |
t1[0] = trq1.x(); |
| 397 |
< |
t1[1] = trq1.y(); |
| 398 |
< |
t1[2] = trq1.z(); |
| 396 |
> |
if (atypes.first->isGayBerne()) { |
| 397 |
> |
GayBerneParam gb1 = getGayBerneParam(atypes.first); |
| 398 |
> |
RealType d1 = gb1.GB_d; |
| 399 |
> |
RealType l1 = gb1.GB_l; |
| 400 |
> |
// sigma is actually sqrt(2)*l for prolate ellipsoids |
| 401 |
> |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
| 402 |
> |
} else if (atypes.first->isLennardJones()) { |
| 403 |
> |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.first)); |
| 404 |
> |
} |
| 405 |
|
|
| 406 |
< |
t2[0] = trq2.x(); |
| 407 |
< |
t2[1] = trq2.y(); |
| 408 |
< |
t2[2] = trq2.z(); |
| 409 |
< |
|
| 410 |
< |
return; |
| 406 |
> |
if (atypes.second->isGayBerne()) { |
| 407 |
> |
GayBerneParam gb2 = getGayBerneParam(atypes.second); |
| 408 |
> |
RealType d2 = gb2.GB_d; |
| 409 |
> |
RealType l2 = gb2.GB_l; |
| 410 |
> |
cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
| 411 |
> |
} else if (atypes.second->isLennardJones()) { |
| 412 |
> |
cut = max(cut, RealType(2.5) * getLJSigma(atypes.second)); |
| 413 |
> |
} |
| 414 |
> |
|
| 415 |
> |
return cut; |
| 416 |
|
} |
| 417 |
|
} |
| 418 |
|
|
| 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 |
– |
} |
