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Comparing branches/development/src/nonbonded/EAM.cpp (file contents):
Revision 1502 by gezelter, Sat Oct 2 19:53:32 2010 UTC vs.
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC

# Line 51 | Line 51 | namespace OpenMD {
51   namespace OpenMD {
52  
53    EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
54 <               mixMeth_(eamJohnson), eamRcut_(0.0) {}
54 >               mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
55    
56    EAMParam EAM::getEAMParam(AtomType* atomType) {
57      
# Line 195 | Line 195 | namespace OpenMD {
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:
# Line 347 | Line 352 | namespace OpenMD {
352      return;
353    }
354  
355 <  void EAM::calcDensity(DensityData ddat) {
355 >  void EAM::calcDensity(InteractionData &idat) {
356      
357      if (!initialized_) initialize();
358      
359 <    EAMAtomData data1 = EAMMap[ddat.atype1];
360 <    EAMAtomData data2 = EAMMap[ddat.atype2];
361 <
362 <    if (ddat.rij < data1.rcut)
363 <      ddat.rho_i_at_j = data1.rho->getValueAt(ddat.rij);
364 <
365 <    if (ddat.rij < data2.rcut)
366 <      ddat.rho_j_at_i = data2.rho->getValueAt(ddat.rij);
367 <
368 <    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 <
376 <  void EAM::calcFunctional(FunctionalData fdat) {
377 <
375 >  
376 >  void EAM::calcFunctional(SelfData &sdat) {
377 >    
378      if (!initialized_) initialize();
379  
380 <    EAMAtomData data1 = EAMMap[fdat.atype];
380 >    EAMAtomData data1 = EAMMap[ sdat.atype ];
381          
382 <    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(fdat.rho);
382 >    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
383  
384 <    fdat.frho = result.first;
385 <    fdat.dfrhodrho = result.second;
384 >    *(sdat.frho) = result.first;
385 >    *(sdat.dfrhodrho) = result.second;
386 >
387 >    (*(sdat.pot))[METALLIC_FAMILY] += result.first;
388 >    *(sdat.particlePot) += result.first;
389 >
390      return;
391    }
392  
393  
394 <  void EAM::calcForce(InteractionData idat) {
394 >  void EAM::calcForce(InteractionData &idat) {
395  
396      if (!initialized_) initialize();
397  
384 –    pair<RealType, RealType> res;
385 –    
386 –    if (idat.rij < eamRcut_) {
398  
388 –      EAMAtomData data1 = EAMMap[idat.atype1];
389 –      EAMAtomData data2 = EAMMap[idat.atype2];
399  
400 <      // get type-specific cutoff radii
401 <
402 <      RealType rci = data1.rcut;
403 <      RealType rcj = data2.rcut;
404 <      
405 <      RealType rha, drha, rhb, drhb;
406 <      RealType pha, dpha, phb, dphb;
407 <      RealType phab, dvpdr;
408 <      RealType drhoidr, drhojdr, dudr;
400 >    if (haveCutoffRadius_)
401 >      if ( *(idat.rij) > eamRcut_) return;
402 >  
403 >    pair<RealType, RealType> res;
404 >    
405 >    
406 >    EAMAtomData data1 = EAMMap[idat.atypes.first];
407 >    EAMAtomData data2 = EAMMap[idat.atypes.second];
408 >    
409 >    // get type-specific cutoff radii
410 >    
411 >    RealType rci = data1.rcut;
412 >    RealType rcj = data2.rcut;
413 >    
414 >    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
415 >    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
416 >    RealType phab(0.0), dvpdr(0.0);
417 >    RealType drhoidr, drhojdr, dudr;
418 >    
419 >    if ( *(idat.rij) < rci) {
420 >      res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
421 >      rha = res.first;
422 >      drha = res.second;
423        
424 <      if (idat.rij < rci) {
425 <        res = data1.rho->getValueAndDerivativeAt(idat.rij);
426 <        rha = res.first;
427 <        drha = res.second;
424 >      res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
425 >      pha = res.first;
426 >      dpha = res.second;
427 >    }
428 >    
429 >    if ( *(idat.rij) < rcj) {
430 >      res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
431 >      rhb = res.first;
432 >      drhb = res.second;
433 >      
434 >      res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
435 >      phb = res.first;
436 >      dphb = res.second;
437 >    }
438  
439 <        res = MixingMap[make_pair(idat.atype1, idat.atype1)].phi->getValueAndDerivativeAt(idat.rij);
440 <        pha = res.first;
441 <        dpha = res.second;
439 >    switch(mixMeth_) {
440 >    case eamJohnson:
441 >      
442 >      if ( *(idat.rij) < rci) {
443 >        phab = phab + 0.5 * (rhb / rha) * pha;
444 >        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
445 >                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
446        }
447 <
448 <      if (idat.rij < rcj) {
449 <        res = data2.rho->getValueAndDerivativeAt(idat.rij);
450 <        rhb = res.first;
451 <        drhb = res.second;
452 <
453 <        res = MixingMap[make_pair(idat.atype2, idat.atype2)].phi->getValueAndDerivativeAt(idat.rij);
417 <        phb = res.first;
418 <        dphb = res.second;
447 >      
448 >      
449 >      
450 >      if ( *(idat.rij) < rcj) {
451 >        phab = phab + 0.5 * (rha / rhb) * phb;
452 >        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
453 >                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
454        }
455 <
456 <      phab = 0.0;
422 <      dvpdr = 0.0;
423 <
424 <      switch(mixMeth_) {
425 <      case eamJohnson:
426 <      
427 <        if (idat.rij < rci) {
428 <          phab = phab + 0.5 * (rhb / rha) * pha;
429 <          dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
430 <                               pha*((drhb/rha) - (rhb*drha/rha/rha)));
431 <        }
432 <
433 <        if (idat.rij < rcj) {
434 <          phab = phab + 0.5 * (rha / rhb) * phb;
435 <          dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
436 <                                 phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
437 <        }
438 <
439 <        break;
440 <
441 <      case eamDaw:
442 <        res = MixingMap[make_pair(idat.atype1,idat.atype2)].phi->getValueAndDerivativeAt(idat.rij);
443 <        phab = res.first;
444 <        dvpdr = res.second;
445 <
446 <        break;
447 <      case eamUnknown:
448 <      default:
449 <
450 <        sprintf(painCave.errMsg,
451 <                "EAM::calcForce hit a mixing method it doesn't know about!\n"
452 <                );
453 <        painCave.severity = OPENMD_ERROR;
454 <        painCave.isFatal = 1;
455 <        simError();        
456 <          
457 <      }
455 >      
456 >      break;
457        
458 <      drhoidr = drha;
459 <      drhojdr = drhb;
458 >    case eamDaw:
459 >      res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
460 >      phab = res.first;
461 >      dvpdr = res.second;
462 >      
463 >      break;
464 >    case eamUnknown:
465 >    default:
466 >      
467 >      sprintf(painCave.errMsg,
468 >              "EAM::calcForce hit a mixing method it doesn't know about!\n"
469 >              );
470 >      painCave.severity = OPENMD_ERROR;
471 >      painCave.isFatal = 1;
472 >      simError();        
473 >      
474 >    }
475 >    
476 >    drhoidr = drha;
477 >    drhojdr = drhb;
478 >    
479 >    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr;
480 >    
481 >    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
482 >        
483 >    // particlePot is the difference between the full potential and
484 >    // the full potential without the presence of a particular
485 >    // particle (atom1).
486 >    //
487 >    // This reduces the density at other particle locations, so we
488 >    // need to recompute the density at atom2 assuming atom1 didn't
489 >    // contribute.  This then requires recomputing the density
490 >    // functional for atom2 as well.
491 >    
492 >    *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha )
493 >      - *(idat.frho2);
494 >    
495 >    *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb)
496 >      - *(idat.frho1);
497 >    
498 >    (*(idat.pot))[METALLIC_FAMILY] += phab;
499 >    
500 >    *(idat.vpair) += phab;
501 >  
502 >    return;
503 >    
504 >  }
505  
506 <      dudr = drhojdr*idat.dfrho1 + drhoidr*idat.dfrho2 + dvpdr;
506 >  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
507 >    if (!initialized_) initialize();  
508  
509 <      idat.f1 = idat.d * dudr / idat.rij;
465 <        
466 <      // particle_pot is the difference between the full potential
467 <      // and the full potential without the presence of a particular
468 <      // particle (atom1).
469 <      //
470 <      // This reduces the density at other particle locations, so
471 <      // we need to recompute the density at atom2 assuming atom1
472 <      // didn't contribute.  This then requires recomputing the
473 <      // density functional for atom2 as well.
474 <      //
475 <      // Most of the particle_pot heavy lifting comes from the
476 <      // pair interaction, and will be handled by vpair.
477 <    
478 <      idat.fshift1 = data1.F->getValueAt( idat.rho1 - rhb );
479 <      idat.fshift2 = data1.F->getValueAt( idat.rho2 - rha );
509 >    RealType cut = 0.0;
510  
511 <      idat.pot += phab;
511 >    map<AtomType*, EAMAtomData>::iterator it;
512  
513 <      idat.vpair += phab;
513 >    it = EAMMap.find(atypes.first);
514 >    if (it != EAMMap.end()) {
515 >      EAMAtomData data1 = (*it).second;
516 >      cut = data1.rcut;
517      }
518  
519 <    return;
520 <    
519 >    it = EAMMap.find(atypes.second);
520 >    if (it != EAMMap.end()) {
521 >      EAMAtomData data2 = (*it).second;
522 >      if (data2.rcut > cut)
523 >        cut = data2.rcut;
524 >    }
525 >
526 >    return cut;
527    }
528   }
529  

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