| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 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, 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> |
| 44 |
#include <string.h> |
| 45 |
|
| 46 |
#include <cmath> |
| 47 |
#include "nonbonded/EAM.hpp" |
| 48 |
#include "utils/simError.h" |
| 49 |
#include "types/NonBondedInteractionType.hpp" |
| 50 |
|
| 51 |
|
| 52 |
namespace OpenMD { |
| 53 |
|
| 54 |
EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), |
| 55 |
mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {} |
| 56 |
|
| 57 |
CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) { |
| 58 |
EAMAdapter ea1 = EAMAdapter(atomType1); |
| 59 |
EAMAdapter ea2 = EAMAdapter(atomType2); |
| 60 |
CubicSpline* z1 = ea1.getZ(); |
| 61 |
CubicSpline* z2 = ea2.getZ(); |
| 62 |
|
| 63 |
// Thise prefactors convert the charge-charge interactions into |
| 64 |
// kcal / mol all were computed assuming distances are measured in |
| 65 |
// angstroms Charge-Charge, assuming charges are measured in |
| 66 |
// electrons. Matches value in Electrostatics.cpp |
| 67 |
pre11_ = 332.0637778; |
| 68 |
|
| 69 |
// make the r grid: |
| 70 |
|
| 71 |
// we need phi out to the largest value we'll encounter in the radial space; |
| 72 |
|
| 73 |
RealType rmax = 0.0; |
| 74 |
rmax = max(rmax, ea1.getRcut()); |
| 75 |
rmax = max(rmax, ea1.getNr() * ea1.getDr()); |
| 76 |
|
| 77 |
rmax = max(rmax, ea2.getRcut()); |
| 78 |
rmax = max(rmax, ea2.getNr() * ea2.getDr()); |
| 79 |
|
| 80 |
// use the smallest dr (finest grid) to build our grid: |
| 81 |
|
| 82 |
RealType dr = min(ea1.getDr(), ea2.getDr()); |
| 83 |
|
| 84 |
int nr = int(rmax/dr + 0.5); |
| 85 |
|
| 86 |
vector<RealType> rvals; |
| 87 |
for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr)); |
| 88 |
|
| 89 |
// construct the pair potential: |
| 90 |
|
| 91 |
vector<RealType> phivals; |
| 92 |
RealType phi; |
| 93 |
RealType r; |
| 94 |
RealType zi, zj; |
| 95 |
|
| 96 |
phivals.push_back(0.0); |
| 97 |
|
| 98 |
for (unsigned int i = 1; i < rvals.size(); i++ ) { |
| 99 |
r = rvals[i]; |
| 100 |
|
| 101 |
// only use z(r) if we're inside this atom's cutoff radius, |
| 102 |
// otherwise, we'll use zero for the charge. This effectively |
| 103 |
// means that our phi grid goes out beyond the cutoff of the |
| 104 |
// pair potential |
| 105 |
|
| 106 |
zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0; |
| 107 |
zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0; |
| 108 |
|
| 109 |
phi = pre11_ * (zi * zj) / r; |
| 110 |
|
| 111 |
phivals.push_back(phi); |
| 112 |
} |
| 113 |
|
| 114 |
CubicSpline* cs = new CubicSpline(); |
| 115 |
cs->addPoints(rvals, phivals); |
| 116 |
return cs; |
| 117 |
} |
| 118 |
|
| 119 |
void EAM::setCutoffRadius( RealType rCut ) { |
| 120 |
eamRcut_ = rCut; |
| 121 |
haveCutoffRadius_ = true; |
| 122 |
} |
| 123 |
|
| 124 |
void EAM::initialize() { |
| 125 |
// set up the mixing method: |
| 126 |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 127 |
string EAMMixMeth = fopts.getEAMMixingMethod(); |
| 128 |
toUpper(EAMMixMeth); |
| 129 |
|
| 130 |
if (EAMMixMeth == "JOHNSON") |
| 131 |
mixMeth_ = eamJohnson; |
| 132 |
else if (EAMMixMeth == "DAW") |
| 133 |
mixMeth_ = eamDaw; |
| 134 |
else |
| 135 |
mixMeth_ = eamUnknown; |
| 136 |
|
| 137 |
// find all of the EAM atom Types: |
| 138 |
EAMtypes.clear(); |
| 139 |
EAMtids.clear(); |
| 140 |
EAMdata.clear(); |
| 141 |
MixingMap.clear(); |
| 142 |
nEAM_ = 0; |
| 143 |
|
| 144 |
EAMtids.resize( forceField_->getNAtomType(), -1); |
| 145 |
|
| 146 |
set<AtomType*>::iterator at; |
| 147 |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 148 |
if ((*at)->isEAM()) nEAM_++; |
| 149 |
} |
| 150 |
EAMdata.resize(nEAM_); |
| 151 |
MixingMap.resize(nEAM_); |
| 152 |
|
| 153 |
for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
| 154 |
if ((*at)->isEAM()) addType(*at); |
| 155 |
} |
| 156 |
|
| 157 |
// find all of the explicit EAM interactions (setfl): |
| 158 |
ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
| 159 |
ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
| 160 |
NonBondedInteractionType* nbt; |
| 161 |
|
| 162 |
for (nbt = nbiTypes->beginType(j); nbt != NULL; |
| 163 |
nbt = nbiTypes->nextType(j)) { |
| 164 |
|
| 165 |
if (nbt->isEAM()) { |
| 166 |
|
| 167 |
pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
| 168 |
|
| 169 |
GenericData* data = nbt->getPropertyByName("EAM"); |
| 170 |
if (data == NULL) { |
| 171 |
sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n" |
| 172 |
"\tEAM parameters for %s - %s interaction.\n", |
| 173 |
atypes.first->getName().c_str(), |
| 174 |
atypes.second->getName().c_str()); |
| 175 |
painCave.severity = OPENMD_ERROR; |
| 176 |
painCave.isFatal = 1; |
| 177 |
simError(); |
| 178 |
} |
| 179 |
|
| 180 |
EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data); |
| 181 |
if (eamData == NULL) { |
| 182 |
sprintf( painCave.errMsg, |
| 183 |
"EAM::rebuildMixingMap could not convert GenericData to\n" |
| 184 |
"\tEAMMixingData for %s - %s interaction.\n", |
| 185 |
atypes.first->getName().c_str(), |
| 186 |
atypes.second->getName().c_str()); |
| 187 |
painCave.severity = OPENMD_ERROR; |
| 188 |
painCave.isFatal = 1; |
| 189 |
simError(); |
| 190 |
} |
| 191 |
|
| 192 |
EAMMixingParam eamParam = eamData->getData(); |
| 193 |
|
| 194 |
vector<RealType> phiAB = eamParam.phi; |
| 195 |
RealType dr = eamParam.dr; |
| 196 |
int nr = eamParam.nr; |
| 197 |
|
| 198 |
addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB); |
| 199 |
} |
| 200 |
} |
| 201 |
initialized_ = true; |
| 202 |
} |
| 203 |
|
| 204 |
|
| 205 |
|
| 206 |
void EAM::addType(AtomType* atomType){ |
| 207 |
|
| 208 |
EAMAdapter ea = EAMAdapter(atomType); |
| 209 |
EAMAtomData eamAtomData; |
| 210 |
|
| 211 |
eamAtomData.rho = ea.getRho(); |
| 212 |
eamAtomData.F = ea.getF(); |
| 213 |
eamAtomData.Z = ea.getZ(); |
| 214 |
eamAtomData.rcut = ea.getRcut(); |
| 215 |
eamAtomData.isFluctuating = atomType->isFluctuatingCharge(); |
| 216 |
|
| 217 |
// add it to the map: |
| 218 |
int atid = atomType->getIdent(); |
| 219 |
int eamtid = EAMtypes.size(); |
| 220 |
|
| 221 |
pair<set<int>::iterator,bool> ret; |
| 222 |
ret = EAMtypes.insert( atid ); |
| 223 |
if (ret.second == false) { |
| 224 |
sprintf( painCave.errMsg, |
| 225 |
"EAM already had a previous entry with ident %d\n", |
| 226 |
atid); |
| 227 |
painCave.severity = OPENMD_INFO; |
| 228 |
painCave.isFatal = 0; |
| 229 |
simError(); |
| 230 |
} |
| 231 |
|
| 232 |
if (eamAtomData.isFluctuating) { |
| 233 |
// compute charge to rho scaling: |
| 234 |
RealType z0 = eamAtomData.Z->getValueAt(0.0); |
| 235 |
RealType dr = ea.getDr(); |
| 236 |
RealType rmax = max(eamAtomData.rcut, ea.getNr() * dr); |
| 237 |
int nr = int(rmax/dr + 0.5); |
| 238 |
RealType r; |
| 239 |
RealType sum(0.0); |
| 240 |
|
| 241 |
for (int i = 0; i < nr; i++) { |
| 242 |
r = RealType(i*dr); |
| 243 |
sum += r * r * eamAtomData.rho->getValueAt(r) * dr; |
| 244 |
} |
| 245 |
sum *= 4.0 * M_PI; |
| 246 |
eamAtomData.qToRhoScaling = sum / z0; |
| 247 |
} |
| 248 |
|
| 249 |
|
| 250 |
EAMtids[atid] = eamtid; |
| 251 |
EAMdata[eamtid] = eamAtomData; |
| 252 |
MixingMap[eamtid].resize(nEAM_); |
| 253 |
|
| 254 |
// Now, iterate over all known types and add to the mixing map: |
| 255 |
|
| 256 |
std::set<int>::iterator it; |
| 257 |
for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) { |
| 258 |
|
| 259 |
int eamtid2 = EAMtids[ (*it) ]; |
| 260 |
AtomType* atype2 = forceField_->getAtomType( (*it) ); |
| 261 |
|
| 262 |
EAMInteractionData mixer; |
| 263 |
mixer.phi = getPhi(atomType, atype2); |
| 264 |
mixer.explicitlySet = false; |
| 265 |
|
| 266 |
MixingMap[eamtid2].resize( nEAM_ ); |
| 267 |
|
| 268 |
MixingMap[eamtid][eamtid2] = mixer; |
| 269 |
if (eamtid2 != eamtid) { |
| 270 |
MixingMap[eamtid2][eamtid] = mixer; |
| 271 |
} |
| 272 |
} |
| 273 |
return; |
| 274 |
} |
| 275 |
|
| 276 |
void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
| 277 |
RealType dr, int nr, |
| 278 |
vector<RealType> phiVals) { |
| 279 |
|
| 280 |
// in case these weren't already in the map |
| 281 |
addType(atype1); |
| 282 |
addType(atype2); |
| 283 |
|
| 284 |
EAMInteractionData mixer; |
| 285 |
CubicSpline* cs = new CubicSpline(); |
| 286 |
vector<RealType> rVals; |
| 287 |
|
| 288 |
for (int i = 0; i < nr; i++) rVals.push_back(i * dr); |
| 289 |
|
| 290 |
cs->addPoints(rVals, phiVals); |
| 291 |
mixer.phi = cs; |
| 292 |
mixer.explicitlySet = true; |
| 293 |
|
| 294 |
int eamtid1 = EAMtids[ atype1->getIdent() ]; |
| 295 |
int eamtid2 = EAMtids[ atype2->getIdent() ]; |
| 296 |
|
| 297 |
MixingMap[eamtid1][eamtid2] = mixer; |
| 298 |
if (eamtid2 != eamtid1) { |
| 299 |
MixingMap[eamtid2][eamtid1] = mixer; |
| 300 |
} |
| 301 |
return; |
| 302 |
} |
| 303 |
|
| 304 |
void EAM::calcDensity(InteractionData &idat) { |
| 305 |
|
| 306 |
if (!initialized_) initialize(); |
| 307 |
|
| 308 |
EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]]; |
| 309 |
EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]]; |
| 310 |
|
| 311 |
if (haveCutoffRadius_) |
| 312 |
if ( *(idat.rij) > eamRcut_) return; |
| 313 |
|
| 314 |
if ( *(idat.rij) < data1.rcut) { |
| 315 |
if (data1.isFluctuating) { |
| 316 |
*(idat.rho2) += (1.0 - *(idat.flucQ1) * data1.qToRhoScaling ) * |
| 317 |
data1.rho->getValueAt( *(idat.rij) ); |
| 318 |
} else { |
| 319 |
*(idat.rho2) += data1.rho->getValueAt( *(idat.rij)); |
| 320 |
} |
| 321 |
} |
| 322 |
|
| 323 |
if ( *(idat.rij) < data2.rcut) { |
| 324 |
if (data2.isFluctuating) { |
| 325 |
*(idat.rho1) += (1.0 - *(idat.flucQ2) * data2.qToRhoScaling ) * |
| 326 |
data2.rho->getValueAt( *(idat.rij) ); |
| 327 |
} else { |
| 328 |
*(idat.rho1) += data2.rho->getValueAt( *(idat.rij)); |
| 329 |
} |
| 330 |
} |
| 331 |
|
| 332 |
return; |
| 333 |
} |
| 334 |
|
| 335 |
void EAM::calcFunctional(SelfData &sdat) { |
| 336 |
|
| 337 |
if (!initialized_) initialize(); |
| 338 |
|
| 339 |
EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ]; |
| 340 |
|
| 341 |
data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), *(sdat.dfrhodrho) ); |
| 342 |
|
| 343 |
(*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho); |
| 344 |
if (sdat.doParticlePot) { |
| 345 |
*(sdat.particlePot) += *(sdat.frho); |
| 346 |
} |
| 347 |
|
| 348 |
return; |
| 349 |
} |
| 350 |
|
| 351 |
|
| 352 |
void EAM::calcForce(InteractionData &idat) { |
| 353 |
|
| 354 |
if (!initialized_) initialize(); |
| 355 |
|
| 356 |
if (haveCutoffRadius_) |
| 357 |
if ( *(idat.rij) > eamRcut_) return; |
| 358 |
|
| 359 |
|
| 360 |
int eamtid1 = EAMtids[idat.atid1]; |
| 361 |
int eamtid2 = EAMtids[idat.atid2]; |
| 362 |
|
| 363 |
EAMAtomData &data1 = EAMdata[eamtid1]; |
| 364 |
EAMAtomData &data2 = EAMdata[eamtid2]; |
| 365 |
|
| 366 |
// get type-specific cutoff radii |
| 367 |
|
| 368 |
RealType rci = data1.rcut; |
| 369 |
RealType rcj = data2.rcut; |
| 370 |
|
| 371 |
RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0); |
| 372 |
RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0); |
| 373 |
RealType phab(0.0), dvpdr(0.0); |
| 374 |
RealType drhoidr, drhojdr, dudr; |
| 375 |
|
| 376 |
if ( *(idat.rij) < rci) { |
| 377 |
data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha); |
| 378 |
CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi; |
| 379 |
phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha); |
| 380 |
if (data1.isFluctuating) { |
| 381 |
*(idat.dVdFQ1) -= *(idat.dfrho2) * rha * data1.qToRhoScaling; |
| 382 |
} |
| 383 |
} |
| 384 |
|
| 385 |
if ( *(idat.rij) < rcj) { |
| 386 |
data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb ); |
| 387 |
CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi; |
| 388 |
phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb); |
| 389 |
if (data2.isFluctuating) { |
| 390 |
*(idat.dVdFQ2) -= *(idat.dfrho1) * rhb * data2.qToRhoScaling; |
| 391 |
} |
| 392 |
} |
| 393 |
|
| 394 |
switch(mixMeth_) { |
| 395 |
case eamJohnson: |
| 396 |
|
| 397 |
if ( *(idat.rij) < rci) { |
| 398 |
phab = phab + 0.5 * (rhb / rha) * pha; |
| 399 |
dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + |
| 400 |
pha*((drhb/rha) - (rhb*drha/rha/rha))); |
| 401 |
} |
| 402 |
|
| 403 |
|
| 404 |
|
| 405 |
if ( *(idat.rij) < rcj) { |
| 406 |
phab = phab + 0.5 * (rha / rhb) * phb; |
| 407 |
dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + |
| 408 |
phb*((drha/rhb) - (rha*drhb/rhb/rhb))); |
| 409 |
} |
| 410 |
|
| 411 |
break; |
| 412 |
|
| 413 |
case eamDaw: |
| 414 |
MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr); |
| 415 |
|
| 416 |
break; |
| 417 |
case eamUnknown: |
| 418 |
default: |
| 419 |
|
| 420 |
sprintf(painCave.errMsg, |
| 421 |
"EAM::calcForce hit a mixing method it doesn't know about!\n" |
| 422 |
); |
| 423 |
painCave.severity = OPENMD_ERROR; |
| 424 |
painCave.isFatal = 1; |
| 425 |
simError(); |
| 426 |
|
| 427 |
} |
| 428 |
|
| 429 |
drhoidr = drha; |
| 430 |
drhojdr = drhb; |
| 431 |
|
| 432 |
dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; |
| 433 |
|
| 434 |
*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
| 435 |
|
| 436 |
|
| 437 |
if (idat.doParticlePot) { |
| 438 |
// particlePot is the difference between the full potential and |
| 439 |
// the full potential without the presence of a particular |
| 440 |
// particle (atom1). |
| 441 |
// |
| 442 |
// This reduces the density at other particle locations, so we |
| 443 |
// need to recompute the density at atom2 assuming atom1 didn't |
| 444 |
// contribute. This then requires recomputing the density |
| 445 |
// functional for atom2 as well. |
| 446 |
|
| 447 |
*(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) |
| 448 |
- *(idat.frho2); |
| 449 |
|
| 450 |
*(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) |
| 451 |
- *(idat.frho1); |
| 452 |
} |
| 453 |
|
| 454 |
(*(idat.pot))[METALLIC_FAMILY] += phab; |
| 455 |
|
| 456 |
*(idat.vpair) += phab; |
| 457 |
|
| 458 |
return; |
| 459 |
|
| 460 |
} |
| 461 |
|
| 462 |
RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
| 463 |
if (!initialized_) initialize(); |
| 464 |
|
| 465 |
RealType cut = 0.0; |
| 466 |
|
| 467 |
int atid1 = atypes.first->getIdent(); |
| 468 |
int atid2 = atypes.second->getIdent(); |
| 469 |
int eamtid1 = EAMtids[atid1]; |
| 470 |
int eamtid2 = EAMtids[atid2]; |
| 471 |
|
| 472 |
if (eamtid1 != -1) { |
| 473 |
EAMAtomData data1 = EAMdata[eamtid1]; |
| 474 |
cut = data1.rcut; |
| 475 |
} |
| 476 |
|
| 477 |
if (eamtid2 != -1) { |
| 478 |
EAMAtomData data2 = EAMdata[eamtid2]; |
| 479 |
if (data2.rcut > cut) |
| 480 |
cut = data2.rcut; |
| 481 |
} |
| 482 |
|
| 483 |
return cut; |
| 484 |
} |
| 485 |
} |
| 486 |
|
