ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/nonbonded/EAM.cpp
(Generate patch)

Comparing:
branches/development/src/nonbonded/EAM.cpp (file contents), Revision 1480 by gezelter, Mon Jul 26 19:50:53 2010 UTC vs.
trunk/src/nonbonded/EAM.cpp (file contents), Revision 2033 by gezelter, Sat Nov 1 14:12:16 2014 UTC

# Line 35 | Line 35
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>
# Line 50 | Line 51 | namespace OpenMD {
51  
52   namespace OpenMD {
53  
54 <  bool EAM::initialized_ = false;
55 <  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 <
54 >  EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
55 >               mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
56    
57 <  EAM* EAM::_instance = NULL;
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 <  EAM* EAM::Instance() {
64 <    if (!_instance) {
65 <      _instance = new EAM();
66 <    }
67 <    return _instance;
69 <  }
70 <  
71 <  EAMParam EAM::getEAMParam(AtomType* atomType) {
72 <    
73 <    // Do sanity checking on the AtomType we were passed before
74 <    // building any data structures:
75 <    if (!atomType->isEAM()) {
76 <      sprintf( painCave.errMsg,
77 <               "EAM::getEAMParam was passed an atomType (%s) that does not\n"
78 <               "\tappear to be an embedded atom method (EAM) atom.\n",
79 <               atomType->getName().c_str());
80 <      painCave.severity = OPENMD_ERROR;
81 <      painCave.isFatal = 1;
82 <      simError();
83 <    }
84 <    
85 <    GenericData* data = atomType->getPropertyByName("EAM");
86 <    if (data == NULL) {
87 <      sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n"
88 <               "\tparameters for atomType %s.\n",
89 <               atomType->getName().c_str());
90 <      painCave.severity = OPENMD_ERROR;
91 <      painCave.isFatal = 1;
92 <      simError();
93 <    }
94 <    
95 <    EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
96 <    if (eamData == NULL) {
97 <      sprintf( painCave.errMsg,
98 <               "EAM::getEAMParam could not convert GenericData to EAMParam for\n"
99 <               "\tatom type %s\n", atomType->getName().c_str());
100 <      painCave.severity = OPENMD_ERROR;
101 <      painCave.isFatal = 1;
102 <      simError();          
103 <    }
104 <    
105 <    return eamData->getData();
106 <  }
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 <  CubicSpline* EAM::getZ(AtomType* atomType) {    
109 <    EAMParam eamParam = getEAMParam(atomType);
110 <    int nr = eamParam.nr;
111 <    RealType dr = eamParam.dr;
112 <    vector<RealType> rvals;
113 <    
114 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
115 <      
116 <    CubicSpline* cs = new CubicSpline();
117 <    cs->addPoints(rvals, eamParam.Z);
118 <    return cs;
119 <  }
69 >    // make the r grid:
70  
71 <  RealType EAM::getRcut(AtomType* atomType) {    
122 <    EAMParam eamParam = getEAMParam(atomType);
123 <    return eamParam.rcut;
124 <  }
125 <
126 <  CubicSpline* EAM::getRho(AtomType* atomType) {    
127 <    EAMParam eamParam = getEAMParam(atomType);
128 <    int nr = eamParam.nr;
129 <    RealType dr = eamParam.dr;
130 <    vector<RealType> rvals;
71 >    // we need phi out to the largest value we'll encounter in the radial space;
72      
73 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
74 <      
75 <    CubicSpline* cs = new CubicSpline();
135 <    cs->addPoints(rvals, eamParam.rho);
136 <    return cs;
137 <  }
73 >    RealType rmax = 0.0;
74 >    rmax = max(rmax, ea1.getRcut());
75 >    rmax = max(rmax, ea1.getNr() * ea1.getDr());
76  
77 <  CubicSpline* EAM::getF(AtomType* atomType) {    
78 <    EAMParam eamParam = getEAMParam(atomType);
141 <    int nrho = eamParam.nrho;
142 <    RealType drho = eamParam.drho;
143 <    vector<RealType> rhovals;
144 <    vector<RealType> scaledF;
145 <    
146 <    for (int i = 0; i < nrho; i++) {
147 <      rhovals.push_back(i * drho);
148 <      scaledF.push_back( eamParam.F[i] * 23.06054 );
149 <    }
150 <      
151 <    CubicSpline* cs = new CubicSpline();
152 <    cs->addPoints(rhovals, eamParam.F);
153 <    return cs;
154 <  }
155 <  
156 <  CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {    
157 <    EAMParam eamParam1 = getEAMParam(atomType1);
158 <    EAMParam eamParam2 = getEAMParam(atomType2);
159 <    CubicSpline* z1 = getZ(atomType1);
160 <    CubicSpline* z2 = getZ(atomType2);
77 >    rmax = max(rmax, ea2.getRcut());
78 >    rmax = max(rmax, ea2.getNr() * ea2.getDr());
79  
80 <    // make the r grid:
80 >    // use the smallest dr (finest grid) to build our grid:
81  
82 <    // set rcut to be the smaller of the two atomic rcuts
82 >    RealType dr = min(ea1.getDr(), ea2.getDr());
83  
84 <    RealType rcut = eamParam1.rcut < eamParam2.rcut ?
167 <      eamParam1.rcut : eamParam2.rcut;
84 >    int nr = int(rmax/dr + 0.5);
85  
169 –    // use the smallest dr (finest grid) to build our grid:
170 –
171 –    RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr;
172 –    int nr = int(rcut/dr);
86      vector<RealType> rvals;
87 <    for (int i = 0; i < nr; i++) rvals.push_back(i*dr);
87 >    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
88  
89      // construct the pair potential:
90  
# Line 182 | Line 95 | namespace OpenMD {
95  
96      phivals.push_back(0.0);
97  
98 <    for (int i = 1; i < rvals.size(); i++ ) {
98 >    for (unsigned int i = 1; i < rvals.size(); i++ ) {
99        r = rvals[i];
187 –      zi = z1->getValueAt(r);
188 –      zj = z2->getValueAt(r);
100  
101 <      phi = 331.999296 * (zi * zj) / r;
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      }
193 –      
113      CubicSpline* cs = new CubicSpline();
114      cs->addPoints(rvals, phivals);
115      return cs;
116    }
117  
118 <  void EAM::initialize() {
118 >  void EAM::setCutoffRadius( RealType rCut ) {
119 >    eamRcut_ = rCut;
120 >    haveCutoffRadius_ = true;
121 >  }
122  
123 +  void EAM::initialize() {
124      // set up the mixing method:
125      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
126 <    std::string EAMMixMeth = fopts.getEAMMixingMethod();
126 >    string EAMMixMeth = fopts.getEAMMixingMethod();
127      toUpper(EAMMixMeth);
128    
129      if (EAMMixMeth == "JOHNSON")
# Line 211 | Line 134 | namespace OpenMD {
134        mixMeth_ = eamUnknown;
135        
136      // find all of the EAM atom Types:
137 <    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
138 <    ForceField::AtomTypeContainer::MapTypeIterator i;
139 <    AtomType* at;
137 >    EAMtypes.clear();
138 >    EAMtids.clear();
139 >    EAMdata.clear();
140 >    MixingMap.clear();
141 >    nEAM_ = 0;
142 >    
143 >    EAMtids.resize( forceField_->getNAtomType(), -1);
144  
145 <    for (at = atomTypes->beginType(i); at != NULL;
146 <         at = atomTypes->nextType(i)) {
147 <      
221 <      if (at->isEAM())
222 <        addType(at);
145 >    set<AtomType*>::iterator at;
146 >    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
147 >      if ((*at)->isEAM()) nEAM_++;
148      }
149 +    EAMdata.resize(nEAM_);
150 +    MixingMap.resize(nEAM_);
151 +
152 +    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
153 +      if ((*at)->isEAM()) addType(*at);
154 +    }
155      
156      // find all of the explicit EAM interactions (setfl):
157      ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
# Line 232 | Line 163 | namespace OpenMD {
163        
164        if (nbt->isEAM()) {
165          
166 <        std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
166 >        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
167          
168          GenericData* data = nbt->getPropertyByName("EAM");
169          if (data == NULL) {
# Line 273 | Line 204 | namespace OpenMD {
204  
205    void EAM::addType(AtomType* atomType){
206  
207 +    EAMAdapter ea = EAMAdapter(atomType);
208      EAMAtomData eamAtomData;
277 –    
278 –    eamAtomData.rho = getRho(atomType);
279 –    eamAtomData.F = getF(atomType);
280 –    eamAtomData.Z = getZ(atomType);
281 –    eamAtomData.rcut = getRcut(atomType);
209  
210 +    eamAtomData.rho = ea.getRho();
211 +    eamAtomData.F = ea.getF();
212 +    eamAtomData.Z = ea.getZ();
213 +    eamAtomData.rcut = ea.getRcut();
214 +      
215      // add it to the map:
216 <    AtomTypeProperties atp = atomType->getATP();    
216 >    int atid = atomType->getIdent();
217 >    int eamtid = EAMtypes.size();
218  
219 <    std::pair<std::map<int,AtomType*>::iterator,bool> ret;    
220 <    ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
219 >    pair<set<int>::iterator,bool> ret;    
220 >    ret = EAMtypes.insert( atid );
221      if (ret.second == false) {
222        sprintf( painCave.errMsg,
223                 "EAM already had a previous entry with ident %d\n",
224 <               atp.ident);
224 >               atid);
225        painCave.severity = OPENMD_INFO;
226        painCave.isFatal = 0;
227        simError();        
228      }
229  
230 <    EAMMap[atomType] = eamAtomData;
230 >
231 >    EAMtids[atid] = eamtid;
232 >    EAMdata[eamtid] = eamAtomData;
233 >    MixingMap[eamtid].resize(nEAM_);
234      
235      // Now, iterate over all known types and add to the mixing map:
236      
237 <    std::map<AtomType*, EAMAtomData>::iterator it;
238 <    for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
237 >    std::set<int>::iterator it;
238 >    for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
239        
240 <      AtomType* atype2 = (*it).first;
240 >      int eamtid2 = EAMtids[ (*it) ];
241 >      AtomType* atype2 = forceField_->getAtomType( (*it) );
242  
243        EAMInteractionData mixer;
244        mixer.phi = getPhi(atomType, atype2);
245 +      mixer.rcut = mixer.phi->getLimits().second;
246        mixer.explicitlySet = false;
247  
248 <      std::pair<AtomType*, AtomType*> key1, key2;
311 <      key1 = std::make_pair(atomType, atype2);
312 <      key2 = std::make_pair(atype2, atomType);
248 >      MixingMap[eamtid2].resize( nEAM_ );
249        
250 <      MixingMap[key1] = mixer;
251 <      if (key2 != key1) {
252 <        MixingMap[key2] = mixer;
250 >      MixingMap[eamtid][eamtid2] = mixer;
251 >      if (eamtid2 != eamtid) {
252 >        MixingMap[eamtid2][eamtid] = mixer;
253        }
254      }      
255      return;
# Line 335 | Line 271 | namespace OpenMD {
271  
272      cs->addPoints(rVals, phiVals);
273      mixer.phi = cs;
274 +    mixer.rcut = mixer.phi->getLimits().second;
275      mixer.explicitlySet = true;
276  
277 <    std::pair<AtomType*, AtomType*> key1, key2;
278 <    key1 = std::make_pair(atype1, atype2);
342 <    key2 = std::make_pair(atype2, atype1);
277 >    int eamtid1 = EAMtids[ atype1->getIdent() ];
278 >    int eamtid2 = EAMtids[ atype2->getIdent() ];
279      
280 <    MixingMap[key1] = mixer;
281 <    if (key2 != key1) {
282 <      MixingMap[key2] = mixer;
280 >    MixingMap[eamtid1][eamtid2] = mixer;
281 >    if (eamtid2 != eamtid1) {
282 >      MixingMap[eamtid2][eamtid1] = mixer;
283      }    
284      return;
285    }
286  
287 <  void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij,
352 <                        RealType &rho_i_at_j, RealType &rho_j_at_i) {
287 >  void EAM::calcDensity(InteractionData &idat) {
288      
289      if (!initialized_) initialize();
290      
291 <    EAMAtomData data1 = EAMMap[at1];
292 <    EAMAtomData data2 = EAMMap[at2];
291 >    EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]];
292 >    EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]];
293  
294 <    if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
295 <    if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
361 <    return;
362 <  }
363 <
364 <  void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho,
365 <                           RealType &dfrhodrho) {
366 <
367 <    if (!initialized_) initialize();
368 <
369 <    EAMAtomData data1 = EAMMap[at1];
370 <        
371 <    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
372 <
373 <    frho = result.first;
374 <    dfrhodrho = result.second;
375 <    return;
376 <  }
377 <
378 <
379 <  void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
380 <                      RealType rij, RealType r2, RealType sw,
381 <                      RealType &vpair, RealType &pot, Vector3d &f1,
382 <                      RealType rho_i, RealType rho_j,
383 <                      RealType dfrhodrho_i, RealType dfrhodrho_j,
384 <                      RealType &fshift_i, RealType &fshift_j) {
385 <
386 <    if (!initialized_) initialize();
294 >    if (haveCutoffRadius_)
295 >      if ( *(idat.rij) > eamRcut_) return;
296      
297 <    pair<RealType, RealType> res;
298 <    
299 <    if (rij < eamRcut_) {
391 <
392 <      EAMAtomData data1 = EAMMap[at1];
393 <      EAMAtomData data2 = EAMMap[at2];
394 <
395 <      // get type-specific cutoff radii
396 <
397 <      RealType rci = data1.rcut;
398 <      RealType rcj = data2.rcut;
297 >    if ( *(idat.rij) < data1.rcut) {
298 >      *(idat.rho2) += data1.rho->getValueAt( *(idat.rij));
299 >    }
300        
301 <      RealType rha, drha, rhb, drhb;
302 <      RealType pha, dpha, phb, dphb;
402 <      RealType phab, dvpdr;
403 <      RealType drhoidr, drhojdr, dudr;
404 <      
405 <      if (rij < rci) {
406 <        res = data1.rho->getValueAndDerivativeAt(rij);
407 <        rha = res.first;
408 <        drha = res.second;
409 <
410 <        res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
411 <        pha = res.first;
412 <        dpha = res.second;
413 <      }
414 <
415 <      if (rij < rcj) {
416 <        res = data2.rho->getValueAndDerivativeAt(rij);
417 <        rhb = res.first;
418 <        drhb = res.second;
419 <
420 <        res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
421 <        phb = res.first;
422 <        dphb = res.second;
423 <      }
424 <
425 <      phab = 0.0;
426 <      dvpdr = 0.0;
427 <
428 <      switch(mixMeth_) {
429 <      case eamJohnson:
430 <      
431 <        if (rij < rci) {
432 <          phab = phab + 0.5 * (rhb / rha) * pha;
433 <          dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
434 <                               pha*((drhb/rha) - (rhb*drha/rha/rha)));
435 <        }
436 <
437 <        if (rij < rcj) {
438 <          phab = phab + 0.5 * (rha / rhb) * phb;
439 <          dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
440 <                                 phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
441 <        }
442 <
443 <        break;
444 <
445 <      case eamDaw:
446 <                
447 <        res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij);
448 <        phab = res.first;
449 <        dvpdr = res.second;
450 <
451 <        break;
452 <      case eamUnknown:
453 <      default:
454 <
455 <        sprintf(painCave.errMsg,
456 <                "EAM::calcForce hit a mixing method it doesn't know about!\n"
457 <                );
458 <        painCave.severity = OPENMD_ERROR;
459 <        painCave.isFatal = 1;
460 <        simError();        
461 <          
462 <      }
463 <      
464 <      drhoidr = drha;
465 <      drhojdr = drhb;
466 <
467 <      dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr;
468 <
469 <      f1 = d * dudr / rij;
470 <        
471 <      // particle_pot is the difference between the full potential
472 <      // and the full potential without the presence of a particular
473 <      // particle (atom1).
474 <      //
475 <      // This reduces the density at other particle locations, so
476 <      // we need to recompute the density at atom2 assuming atom1
477 <      // didn't contribute.  This then requires recomputing the
478 <      // density functional for atom2 as well.
479 <      //
480 <      // Most of the particle_pot heavy lifting comes from the
481 <      // pair interaction, and will be handled by vpair.
482 <    
483 <      fshift_i = data1.F->getValueAt( rho_i - rhb );
484 <      fshift_j = data1.F->getValueAt( rho_j - rha );
485 <
486 <      pot += phab;
487 <
488 <      vpair += phab;
301 >    if ( *(idat.rij) < data2.rcut) {
302 >      *(idat.rho1) += data2.rho->getValueAt( *(idat.rij));
303      }
490 –
491 –    return;
304      
305 +    return;  
306    }
307 <
308 <
496 <  void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij,
497 <                                 RealType* rho_i_at_j, RealType* rho_j_at_i){
498 <
499 <    if (!initialized_) initialize();
307 >  
308 >  void EAM::calcFunctional(SelfData &sdat) {
309      
310 <    AtomType* atype1 = EAMlist[*atid1];
311 <    AtomType* atype2 = EAMlist[*atid2];
312 <    
313 <    calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i);
310 >    if (!initialized_) initialize();
311 >    EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ];
312 >            
313 >    data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho),
314 >                                      *(sdat.dfrhodrho) );
315  
316 <    return;    
316 >    (*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho);
317 >    if (sdat.doParticlePot) {
318 >      *(sdat.particlePot) += *(sdat.frho);
319 >    }
320 >
321 >    return;
322    }
323  
324 <  void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho,
325 <                                   RealType *dfrhodrho) {
324 >
325 >  void EAM::calcForce(InteractionData &idat) {
326  
327      if (!initialized_) initialize();
328  
329 <    AtomType* atype1 = EAMlist[*atid1];  
329 >    if (haveCutoffRadius_)
330 >      if ( *(idat.rij) > eamRcut_) return;
331 >  
332  
333 <    calcFunctional(atype1, *rho, *frho, *dfrhodrho);
333 >    int eamtid1 = EAMtids[idat.atid1];
334 >    int eamtid2 = EAMtids[idat.atid2];
335 >    EAMAtomData &data1 = EAMdata[eamtid1];
336 >    EAMAtomData &data2 = EAMdata[eamtid2];
337      
338 <    return;    
519 <  }
520 <  RealType EAM::getEAMcut(int *atid1) {
521 <
522 <    if (!initialized_) initialize();
338 >    // get type-specific cutoff radii
339      
340 <    AtomType* atype1 = EAMlist[*atid1];  
341 <      
526 <    return getRcut(atype1);
527 <  }
340 >    RealType rci = data1.rcut;
341 >    RealType rcj = data2.rcut;
342  
529 –  void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij,
530 –                        RealType *r2, RealType *sw, RealType *vpair,
531 –                        RealType *pot, RealType *f1, RealType *rho1,
532 –                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
533 –                        RealType *fshift1, RealType *fshift2) {
534 –
535 –    if (!initialized_) initialize();
343      
344 <    AtomType* atype1 = EAMlist[*atid1];
345 <    AtomType* atype2 = EAMlist[*atid2];
344 >    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
345 >    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
346 >    RealType phab(0.0), dvpdr(0.0);
347 >    RealType drhoidr, drhojdr, dudr;
348      
349 <    Vector3d disp(d[0], d[1], d[2]);
350 <    Vector3d frc(f1[0], f1[1], f1[2]);
349 >    if ( *(idat.rij) < rci) {
350 >      data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha);
351 >      CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi;
352 >      phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha);
353 >    }
354      
355 <    calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair,  *pot, frc,
356 <              *rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2);
355 >    if ( *(idat.rij) < rcj) {
356 >      data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
357 >      CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
358 >      phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
359 >    }
360 >    switch(mixMeth_) {
361 >    case eamJohnson:
362 >      if ( *(idat.rij) < rci) {
363 >        phab = phab + 0.5 * (rhb / rha) * pha;
364 >        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
365 >                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
366 >      }
367 >                
368 >      if ( *(idat.rij) < rcj) {
369 >        phab = phab + 0.5 * (rha / rhb) * phb;
370 >        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
371 >                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
372 >      }
373 >      break;
374 >    case eamDaw:
375 >      if ( *(idat.rij) <  MixingMap[eamtid1][eamtid2].rcut) {
376 >        MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij),
377 >                                                                  phab, dvpdr);
378 >      }
379 >      break;
380 >    case eamUnknown:
381 >    default:
382        
383 <    f1[0] = frc.x();
384 <    f1[1] = frc.y();
385 <    f1[2] = frc.z();
383 >      sprintf(painCave.errMsg,
384 >              "EAM::calcForce hit a mixing method it doesn't know about!\n"
385 >              );
386 >      painCave.severity = OPENMD_ERROR;
387 >      painCave.isFatal = 1;
388 >      simError();        
389 >      
390 >    }
391 >    
392 >    drhoidr = drha;
393 >    drhojdr = drhb;
394 >    
395 >    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr;
396 >    
397 >    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
398  
399 +    if (idat.doParticlePot) {
400 +      // particlePot is the difference between the full potential and
401 +      // the full potential without the presence of a particular
402 +      // particle (atom1).
403 +      //
404 +      // This reduces the density at other particle locations, so we
405 +      // need to recompute the density at atom2 assuming atom1 didn't
406 +      // contribute.  This then requires recomputing the density
407 +      // functional for atom2 as well.
408 +      
409 +      *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha )
410 +        - *(idat.frho2);
411 +      
412 +      *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb)
413 +        - *(idat.frho1);
414 +    }
415 +    
416 +    (*(idat.pot))[METALLIC_FAMILY] += phab;    
417 +    *(idat.vpair) += phab;  
418      return;    
419    }
552 –  
553 –  void EAM::setCutoffEAM(RealType *thisRcut) {
554 –    eamRcut_ = *thisRcut;
555 –  }
556 – }
420  
421 < extern "C" {
422 <  
560 < #define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
561 < #define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
562 < #define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
563 < #define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
564 < #define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT)
421 >  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
422 >    if (!initialized_) initialize();  
423  
424 <  
425 <  void fortranCalcDensity(int *atid1, int *atid2, RealType *rij,
426 <                          RealType *rho_i_at_j, RealType *rho_j_at_i) {
424 >    RealType cut = 0.0;
425 >
426 >    int atid1 = atypes.first->getIdent();
427 >    int atid2 = atypes.second->getIdent();
428 >    int eamtid1 = EAMtids[atid1];
429 >    int eamtid2 = EAMtids[atid2];
430      
431 <    return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij,
432 <                                                         rho_i_at_j,  
433 <                                                         rho_j_at_i);
434 <  }
435 <  void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho,
436 <                             RealType *dfrhodrho) {  
431 >    if (eamtid1 != -1) {
432 >      EAMAtomData data1 = EAMdata[eamtid1];
433 >      cut = data1.rcut;
434 >    }
435 >
436 >    if (eamtid2 != -1) {
437 >      EAMAtomData data2 = EAMdata[eamtid2];
438 >      if (data2.rcut > cut)
439 >        cut = data2.rcut;
440 >    }
441      
442 <    return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho,
578 <                                                           dfrhodrho);
579 <    
442 >    return cut;
443    }
581 –  void fortranSetCutoffEAM(RealType *rcut) {
582 –    return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
583 –  }
584 –  void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij,
585 –                        RealType *r2, RealType *sw, RealType *vpair,
586 –                        RealType *pot, RealType *f1, RealType *rho1,
587 –                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
588 –                        RealType *fshift1, RealType *fshift2){
589 –    
590 –    return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij,
591 –                                                r2, sw, vpair,
592 –                                                pot, f1, rho1,
593 –                                                rho2, dfrho1, dfrho2,
594 –                                                fshift1,  fshift2);
595 –  }
596 –  RealType fortranGetEAMcut(int* atid) {
597 –    return OpenMD::EAM::Instance()->getEAMcut(atid);
598 –  }
599 –
444   }
445 +

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines