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Comparing branches/development/src/nonbonded/EAM.cpp (file contents):
Revision 1479 by gezelter, Mon Jul 26 19:00:48 2010 UTC vs.
Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

# Line 50 | Line 50 | namespace OpenMD {
50  
51   namespace OpenMD {
52  
53 <  bool EAM::initialized_ = false;
54 <  RealType EAM::eamRcut_ = 0.0;
55 <  EAMMixingMethod EAM::mixMeth_ = eamJohnson;
56 <  ForceField* EAM::forceField_ = NULL;
57 <  std::map<int, AtomType*> EAM::EAMlist;
58 <  std::map<AtomType*, EAMAtomData> EAM::EAMMap;
59 <  std::map<std::pair<AtomType*, AtomType*>, EAMInteractionData> EAM::MixingMap;
60 <
53 >  EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
54 >               mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
55    
62 –  EAM* EAM::_instance = NULL;
63 –
64 –  EAM* EAM::Instance() {
65 –    if (!_instance) {
66 –      _instance = new EAM();
67 –    }
68 –    return _instance;
69 –  }
70 –  
56    EAMParam EAM::getEAMParam(AtomType* atomType) {
57      
58      // Do sanity checking on the AtomType we were passed before
# Line 111 | Line 96 | namespace OpenMD {
96      RealType dr = eamParam.dr;
97      vector<RealType> rvals;
98      
99 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
99 >    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
100        
101      CubicSpline* cs = new CubicSpline();
102      cs->addPoints(rvals, eamParam.Z);
# Line 129 | Line 114 | namespace OpenMD {
114      RealType dr = eamParam.dr;
115      vector<RealType> rvals;
116      
117 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
117 >    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
118        
119      CubicSpline* cs = new CubicSpline();
120      cs->addPoints(rvals, eamParam.rho);
# Line 144 | Line 129 | namespace OpenMD {
129      vector<RealType> scaledF;
130      
131      for (int i = 0; i < nrho; i++) {
132 <      rhovals.push_back(i * drho);
132 >      rhovals.push_back(RealType(i) * drho);
133        scaledF.push_back( eamParam.F[i] * 23.06054 );
134      }
135        
136      CubicSpline* cs = new CubicSpline();
137 <    cs->addPoints(rhovals, eamParam.F);
137 >    cs->addPoints(rhovals, scaledF);
138      return cs;
139    }
140    
# Line 161 | Line 146 | namespace OpenMD {
146  
147      // make the r grid:
148  
164 –    // set rcut to be the smaller of the two atomic rcuts
149  
150 <    RealType rcut = eamParam1.rcut < eamParam2.rcut ?
151 <      eamParam1.rcut : eamParam2.rcut;
150 >    // we need phi out to the largest value we'll encounter in the radial space;
151 >    
152 >    RealType rmax = 0.0;
153 >    rmax = max(rmax, eamParam1.rcut);
154 >    rmax = max(rmax, eamParam1.nr * eamParam1.dr);
155  
156 +    rmax = max(rmax, eamParam2.rcut);
157 +    rmax = max(rmax, eamParam2.nr * eamParam2.dr);
158 +
159      // use the smallest dr (finest grid) to build our grid:
160  
161 <    RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr;
162 <    int nr = int(rcut/dr);
161 >    RealType dr = min(eamParam1.dr, eamParam2.dr);
162 >
163 >    int nr = int(rmax/dr + 0.5);
164 >
165      vector<RealType> rvals;
166 <    for (int i = 0; i < nr; i++) rvals.push_back(i*dr);
166 >    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
167  
168      // construct the pair potential:
169  
# Line 184 | Line 176 | namespace OpenMD {
176  
177      for (int i = 1; i < rvals.size(); i++ ) {
178        r = rvals[i];
187 –      zi = z1->getValueAt(r);
188 –      zj = z2->getValueAt(r);
179  
180 +      // only use z(r) if we're inside this atom's cutoff radius,
181 +      // otherwise, we'll use zero for the charge.  This effectively
182 +      // means that our phi grid goes out beyond the cutoff of the
183 +      // pair potential
184 +
185 +      zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0;
186 +      zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0;
187 +
188        phi = 331.999296 * (zi * zj) / r;
189 +
190        phivals.push_back(phi);
191      }
192        
193      CubicSpline* cs = new CubicSpline();
194      cs->addPoints(rvals, phivals);
195      return cs;
196 +  }
197 +
198 +  void EAM::setCutoffRadius( RealType rCut ) {
199 +    eamRcut_ = rCut;
200 +    haveCutoffRadius_ = true;
201    }
202  
203    void EAM::initialize() {
204  
205      // set up the mixing method:
206      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
207 <    string EAMMixMeth = toUpperCopy(fopts.getEAMMixingMethod());
208 <
207 >    string EAMMixMeth = fopts.getEAMMixingMethod();
208 >    toUpper(EAMMixMeth);
209 >  
210      if (EAMMixMeth == "JOHNSON")
211        mixMeth_ = eamJohnson;    
212      else if (EAMMixMeth == "DAW")
# Line 231 | Line 236 | namespace OpenMD {
236        
237        if (nbt->isEAM()) {
238          
239 <        std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
239 >        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
240          
241          GenericData* data = nbt->getPropertyByName("EAM");
242          if (data == NULL) {
# Line 282 | Line 287 | namespace OpenMD {
287      // add it to the map:
288      AtomTypeProperties atp = atomType->getATP();    
289  
290 <    std::pair<std::map<int,AtomType*>::iterator,bool> ret;    
291 <    ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
290 >    pair<map<int,AtomType*>::iterator,bool> ret;    
291 >    ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) );
292      if (ret.second == false) {
293        sprintf( painCave.errMsg,
294                 "EAM already had a previous entry with ident %d\n",
# Line 297 | Line 302 | namespace OpenMD {
302      
303      // Now, iterate over all known types and add to the mixing map:
304      
305 <    std::map<AtomType*, EAMAtomData>::iterator it;
305 >    map<AtomType*, EAMAtomData>::iterator it;
306      for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
307        
308        AtomType* atype2 = (*it).first;
# Line 306 | Line 311 | namespace OpenMD {
311        mixer.phi = getPhi(atomType, atype2);
312        mixer.explicitlySet = false;
313  
314 <      std::pair<AtomType*, AtomType*> key1, key2;
315 <      key1 = std::make_pair(atomType, atype2);
316 <      key2 = std::make_pair(atype2, atomType);
314 >      pair<AtomType*, AtomType*> key1, key2;
315 >      key1 = make_pair(atomType, atype2);
316 >      key2 = make_pair(atype2, atomType);
317        
318        MixingMap[key1] = mixer;
319        if (key2 != key1) {
# Line 336 | Line 341 | namespace OpenMD {
341      mixer.phi = cs;
342      mixer.explicitlySet = true;
343  
344 <    std::pair<AtomType*, AtomType*> key1, key2;
345 <    key1 = std::make_pair(atype1, atype2);
346 <    key2 = std::make_pair(atype2, atype1);
344 >    pair<AtomType*, AtomType*> key1, key2;
345 >    key1 = make_pair(atype1, atype2);
346 >    key2 = make_pair(atype2, atype1);
347      
348      MixingMap[key1] = mixer;
349      if (key2 != key1) {
# Line 347 | Line 352 | namespace OpenMD {
352      return;
353    }
354  
355 <  void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij,
351 <                        RealType &rho_i_at_j, RealType &rho_j_at_i) {
355 >  void EAM::calcDensity(InteractionData &idat) {
356      
357      if (!initialized_) initialize();
358      
359 <    EAMAtomData data1 = EAMMap[at1];
360 <    EAMAtomData data2 = EAMMap[at2];
361 <
362 <    if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
363 <    if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
364 <    return;
359 >    EAMAtomData data1 = EAMMap[idat.atypes.first];
360 >    EAMAtomData data2 = EAMMap[idat.atypes.second];
361 >    
362 >    if (haveCutoffRadius_)
363 >      if ( *(idat.rij) > eamRcut_) return;
364 >    
365 >    if ( *(idat.rij) < data1.rcut)
366 >      *(idat.rho1) += data1.rho->getValueAt( *(idat.rij));
367 >    
368 >      
369 >    if ( *(idat.rij) < data2.rcut)
370 >      *(idat.rho2) += data2.rho->getValueAt( *(idat.rij));
371 >    
372 >    return;  
373    }
374 <
375 <  void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho,
376 <                           RealType &dfrhodrho) {
365 <
374 >  
375 >  void EAM::calcFunctional(SelfData &sdat) {
376 >    
377      if (!initialized_) initialize();
378  
379 <    EAMAtomData data1 = EAMMap[at1];
379 >    EAMAtomData data1 = EAMMap[ sdat.atype ];
380          
381 <    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
381 >    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
382  
383 <    frho = result.first;
384 <    dfrhodrho = result.second;
383 >    *(sdat.frho) = result.first;
384 >    *(sdat.dfrhodrho) = result.second;
385 >
386 >    (*(sdat.pot))[METALLIC_FAMILY] += result.first;
387 >    *(sdat.particlePot) += result.first;
388 >
389      return;
390    }
391  
392  
393 <  void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
379 <                      RealType rij, RealType r2, RealType sw,
380 <                      RealType &vpair, RealType &pot, Vector3d &f1,
381 <                      RealType rho_i, RealType rho_j,
382 <                      RealType dfrhodrho_i, RealType dfrhodrho_j,
383 <                      RealType &fshift_i, RealType &fshift_j) {
393 >  void EAM::calcForce(InteractionData &idat) {
394  
395      if (!initialized_) initialize();
396 <    
396 >
397 >    if (haveCutoffRadius_)
398 >      if ( *(idat.rij) > eamRcut_) return;
399 >  
400      pair<RealType, RealType> res;
401      
402 <    if (rij < eamRcut_) {
403 <
404 <      EAMAtomData data1 = EAMMap[at1];
405 <      EAMAtomData data2 = EAMMap[at2];
406 <
407 <      // get type-specific cutoff radii
408 <
409 <      RealType rci = data1.rcut;
410 <      RealType rcj = data2.rcut;
402 >    EAMAtomData data1 = EAMMap[idat.atypes.first];
403 >    EAMAtomData data2 = EAMMap[idat.atypes.second];
404 >    
405 >    // get type-specific cutoff radii
406 >    
407 >    RealType rci = data1.rcut;
408 >    RealType rcj = data2.rcut;
409 >    
410 >    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
411 >    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
412 >    RealType phab(0.0), dvpdr(0.0);
413 >    RealType drhoidr, drhojdr, dudr;
414 >    
415 >    if ( *(idat.rij) < rci) {
416 >      res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
417 >      rha = res.first;
418 >      drha = res.second;
419        
420 <      RealType rha, drha, rhb, drhb;
421 <      RealType pha, dpha, phb, dphb;
422 <      RealType phab, dvpdr;
423 <      RealType drhoidr, drhojdr, dudr;
420 >      res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
421 >      pha = res.first;
422 >      dpha = res.second;
423 >    }
424 >    
425 >    if ( *(idat.rij) < rcj) {
426 >      res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
427 >      rhb = res.first;
428 >      drhb = res.second;
429        
430 <      if (rij < rci) {
431 <        res = data1.rho->getValueAndDerivativeAt(rij);
432 <        rha = res.first;
433 <        drha = res.second;
430 >      res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
431 >      phb = res.first;
432 >      dphb = res.second;
433 >    }
434  
435 <        res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
436 <        pha = res.first;
437 <        dpha = res.second;
435 >    switch(mixMeth_) {
436 >    case eamJohnson:
437 >      
438 >      if ( *(idat.rij) < rci) {
439 >        phab = phab + 0.5 * (rhb / rha) * pha;
440 >        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
441 >                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
442        }
443 <
444 <      if (rij < rcj) {
445 <        res = data2.rho->getValueAndDerivativeAt(rij);
446 <        rhb = res.first;
447 <        drhb = res.second;
448 <
449 <        res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
420 <        phb = res.first;
421 <        dphb = res.second;
422 <      }
423 <
424 <      phab = 0.0;
425 <      dvpdr = 0.0;
426 <
427 <      switch(mixMeth_) {
428 <      case eamJohnson:
429 <      
430 <        if (rij < rci) {
431 <          phab = phab + 0.5 * (rhb / rha) * pha;
432 <          dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
433 <                               pha*((drhb/rha) - (rhb*drha/rha/rha)));
434 <        }
435 <
436 <        if (rij < rcj) {
437 <          phab = phab + 0.5 * (rha / rhb) * phb;
438 <          dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
439 <                                 phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
440 <        }
441 <
442 <        break;
443 <
444 <      case eamDaw:
445 <                
446 <        res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij);
447 <        phab = res.first;
448 <        dvpdr = res.second;
449 <
450 <        break;
451 <      case eamUnknown:
452 <      default:
453 <
454 <        sprintf(painCave.errMsg,
455 <                "EAM::calcForce hit a mixing method it doesn't know about!\n"
456 <                );
457 <        painCave.severity = OPENMD_ERROR;
458 <        painCave.isFatal = 1;
459 <        simError();        
460 <          
443 >      
444 >      
445 >      
446 >      if ( *(idat.rij) < rcj) {
447 >        phab = phab + 0.5 * (rha / rhb) * phb;
448 >        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
449 >                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
450        }
451        
452 <      drhoidr = drha;
453 <      drhojdr = drhb;
454 <
455 <      dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr;
456 <
457 <      f1 = d * dudr / rij;
458 <        
459 <      // particle_pot is the difference between the full potential
460 <      // and the full potential without the presence of a particular
461 <      // particle (atom1).
462 <      //
463 <      // This reduces the density at other particle locations, so
464 <      // we need to recompute the density at atom2 assuming atom1
465 <      // didn't contribute.  This then requires recomputing the
466 <      // density functional for atom2 as well.
467 <      //
468 <      // Most of the particle_pot heavy lifting comes from the
469 <      // pair interaction, and will be handled by vpair.
481 <    
482 <      fshift_i = data1.F->getValueAt( rho_i - rhb );
483 <      fshift_j = data1.F->getValueAt( rho_j - rha );
484 <
485 <      pot += phab;
486 <
487 <      vpair += phab;
452 >      break;
453 >      
454 >    case eamDaw:
455 >      res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
456 >      phab = res.first;
457 >      dvpdr = res.second;
458 >      
459 >      break;
460 >    case eamUnknown:
461 >    default:
462 >      
463 >      sprintf(painCave.errMsg,
464 >              "EAM::calcForce hit a mixing method it doesn't know about!\n"
465 >              );
466 >      painCave.severity = OPENMD_ERROR;
467 >      painCave.isFatal = 1;
468 >      simError();        
469 >      
470      }
489 –
490 –    return;
471      
472 <  }
473 <
494 <
495 <  void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij,
496 <                                 RealType* rho_i_at_j, RealType* rho_j_at_i){
497 <
498 <    if (!initialized_) initialize();
472 >    drhoidr = drha;
473 >    drhojdr = drhb;
474      
475 <    AtomType* atype1 = EAMlist[*atid1];
501 <    AtomType* atype2 = EAMlist[*atid2];
475 >    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr;
476      
477 <    calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i);
478 <
479 <    return;    
480 <  }
481 <
482 <  void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho,
483 <                                   RealType *dfrhodrho) {
484 <
485 <    if (!initialized_) initialize();
486 <
513 <    AtomType* atype1 = EAMlist[*atid1];  
514 <
515 <    calcFunctional(atype1, *rho, *frho, *dfrhodrho);
477 >    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
478 >        
479 >    // particlePot is the difference between the full potential and
480 >    // the full potential without the presence of a particular
481 >    // particle (atom1).
482 >    //
483 >    // This reduces the density at other particle locations, so we
484 >    // need to recompute the density at atom2 assuming atom1 didn't
485 >    // contribute.  This then requires recomputing the density
486 >    // functional for atom2 as well.
487      
488 <    return;    
489 <  }
519 <  RealType EAM::getEAMcut(int *atid1) {
520 <
521 <    if (!initialized_) initialize();
488 >    *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha )
489 >      - *(idat.frho2);
490      
491 <    AtomType* atype1 = EAMlist[*atid1];  
492 <      
525 <    return getRcut(atype1);
526 <  }
527 <
528 <  void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij,
529 <                        RealType *r2, RealType *sw, RealType *vpair,
530 <                        RealType *pot, RealType *f1, RealType *rho1,
531 <                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
532 <                        RealType *fshift1, RealType *fshift2) {
533 <
534 <    if (!initialized_) initialize();
491 >    *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb)
492 >      - *(idat.frho1);
493      
494 <    AtomType* atype1 = EAMlist[*atid1];
537 <    AtomType* atype2 = EAMlist[*atid2];
494 >    (*(idat.pot))[METALLIC_FAMILY] += phab;
495      
496 <    Vector3d disp(d[0], d[1], d[2]);
497 <    Vector3d frc(f1[0], f1[1], f1[2]);
496 >    *(idat.vpair) += phab;
497 >  
498 >    return;
499      
542 –    calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair,  *pot, frc,
543 –              *rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2);
544 –      
545 –    f1[0] = frc.x();
546 –    f1[1] = frc.y();
547 –    f1[2] = frc.z();
548 –
549 –    return;    
500    }
551 –  
552 –  void EAM::setCutoffEAM(RealType *thisRcut) {
553 –    eamRcut_ = *thisRcut;
554 –  }
555 – }
501  
502 < extern "C" {
503 <  
559 < #define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
560 < #define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
561 < #define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
562 < #define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
563 < #define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT)
502 >  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
503 >    if (!initialized_) initialize();  
504  
505 <  
566 <  void fortranCalcDensity(int *atid1, int *atid2, RealType *rij,
567 <                          RealType *rho_i_at_j, RealType *rho_j_at_i) {
568 <    
569 <    return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij,
570 <                                                         rho_i_at_j,  
571 <                                                         rho_j_at_i);
572 <  }
573 <  void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho,
574 <                             RealType *dfrhodrho) {  
575 <    
576 <    return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho,
577 <                                                           dfrhodrho);
578 <    
579 <  }
580 <  void fortranSetCutoffEAM(RealType *rcut) {
581 <    return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
582 <  }
583 <  void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij,
584 <                        RealType *r2, RealType *sw, RealType *vpair,
585 <                        RealType *pot, RealType *f1, RealType *rho1,
586 <                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
587 <                        RealType *fshift1, RealType *fshift2){
588 <    
589 <    return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij,
590 <                                                r2, sw, vpair,
591 <                                                pot, f1, rho1,
592 <                                                rho2, dfrho1, dfrho2,
593 <                                                fshift1,  fshift2);
594 <  }
595 <  RealType fortranGetEAMcut(int* atid) {
596 <    return OpenMD::EAM::Instance()->getEAMcut(atid);
597 <  }
505 >    RealType cut = 0.0;
506  
507 +    map<AtomType*, EAMAtomData>::iterator it;
508 +
509 +    it = EAMMap.find(atypes.first);
510 +    if (it != EAMMap.end()) {
511 +      EAMAtomData data1 = (*it).second;
512 +      cut = data1.rcut;
513 +    }
514 +
515 +    it = EAMMap.find(atypes.second);
516 +    if (it != EAMMap.end()) {
517 +      EAMAtomData data2 = (*it).second;
518 +      if (data2.rcut > cut)
519 +        cut = data2.rcut;
520 +    }
521 +
522 +    return cut;
523 +  }
524   }
525 +

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