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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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Comparing trunk/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

# Line 89 | Line 89 | namespace OpenMD {
89      repulsivePower_->setForceField(forceField_);
90  
91      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92 +    int nTypes = atomTypes->size();
93 +    iHash_.resize(nTypes);
94 +    interactions_.resize(nTypes);
95      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
96      AtomType* atype1;
97      AtomType* atype2;
98 <    pair<AtomType*, AtomType*> key;
98 >    int atid1, atid2;
99 >
100 >    // We only need to worry about the types that are actually in the simulation:
101 >
102 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
103 >
104 >    lj_->setSimulatedAtomTypes(atypes);
105 >    gb_->setSimulatedAtomTypes(atypes);
106 >    sticky_->setSimulatedAtomTypes(atypes);
107 >    eam_->setSimulatedAtomTypes(atypes);
108 >    sc_->setSimulatedAtomTypes(atypes);
109 >    morse_->setSimulatedAtomTypes(atypes);
110 >    electrostatic_->setSimInfo(info_);
111 >    electrostatic_->setSimulatedAtomTypes(atypes);
112 >    maw_->setSimulatedAtomTypes(atypes);
113 >    repulsivePower_->setSimulatedAtomTypes(atypes);
114 >
115 >    set<AtomType*>::iterator at;
116 >
117 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
118      
119 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 <         atype1 = atomTypes->nextType(i1)) {
119 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 >      //   atype1 = atomTypes->nextType(i1)) {
121        
122 <      // add it to the map:
123 <      
122 >      atype1 = *at;
123 >      atid1 = atype1->getIdent();
124 >      iHash_[atid1].resize(nTypes);
125 >      interactions_[atid1].resize(nTypes);
126 >
127 >      // add it to the map:      
128        pair<map<int,AtomType*>::iterator,bool> ret;    
129 <      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
129 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
130        if (ret.second == false) {
131          sprintf( painCave.errMsg,
132                   "InteractionManager already had a previous entry with ident %d\n",
# Line 116 | Line 142 | namespace OpenMD {
142      map<int, AtomType*>::iterator it1, it2;
143      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
144        atype1 = (*it1).second;
145 +      atid1 = atype1->getIdent();
146  
147        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
148          atype2 = (*it2).second;
149 +        atid2 = atype2->getIdent();
150                                
151 <        key = make_pair(atype1, atype2);
124 <
125 <        iHash_[key] = 0;
151 >        iHash_[atid1][atid2] = 0;
152          
153          if (atype1->isLennardJones() && atype2->isLennardJones()) {
154 <          interactions_[key].insert(lj_);
155 <          iHash_[key] |= LJ_PAIR;
154 >          interactions_[atid1][atid2].insert(lj_);
155 >          iHash_[atid1][atid2] |= LJ_PAIR;
156          }
157          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158 <          interactions_[key].insert(electrostatic_);
159 <          iHash_[key] |= ELECTROSTATIC_PAIR;
158 >          interactions_[atid1][atid2].insert(electrostatic_);
159 >          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
160          }
161          if (atype1->isSticky() && atype2->isSticky() ) {
162 <          interactions_[key].insert(sticky_);
163 <          iHash_[key] |= STICKY_PAIR;
162 >          interactions_[atid1][atid2].insert(sticky_);
163 >          iHash_[atid1][atid2] |= STICKY_PAIR;
164          }
165          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166 <          interactions_[key].insert(sticky_);
167 <          iHash_[key] |= STICKY_PAIR;
166 >          interactions_[atid1][atid2].insert(sticky_);
167 >          iHash_[atid1][atid2] |= STICKY_PAIR;
168          }
169          if (atype1->isEAM() && atype2->isEAM() ) {
170 <          interactions_[key].insert(eam_);
171 <          iHash_[key] |= EAM_PAIR;
170 >          interactions_[atid1][atid2].insert(eam_);
171 >          iHash_[atid1][atid2] |= EAM_PAIR;
172          }
173          if (atype1->isSC() && atype2->isSC() ) {
174 <          interactions_[key].insert(sc_);
175 <          iHash_[key] |= SC_PAIR;
174 >          interactions_[atid1][atid2].insert(sc_);
175 >          iHash_[atid1][atid2] |= SC_PAIR;
176          }
177          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178 <          interactions_[key].insert(gb_);
179 <          iHash_[key] |= GB_PAIR;
178 >          interactions_[atid1][atid2].insert(gb_);
179 >          iHash_[atid1][atid2] |= GB_PAIR;
180          }
181          if ((atype1->isGayBerne() && atype2->isLennardJones())
182              || (atype1->isLennardJones() && atype2->isGayBerne())) {
183 <          interactions_[key].insert(gb_);
184 <          iHash_[key] |= GB_PAIR;
183 >          interactions_[atid1][atid2].insert(gb_);
184 >          iHash_[atid1][atid2] |= GB_PAIR;
185          }
186          
187          // look for an explicitly-set non-bonded interaction type using the
# Line 172 | Line 198 | namespace OpenMD {
198              // We found an explicit Lennard-Jones interaction.  
199              // override all other vdw entries for this pair of atom types:
200              set<NonBondedInteraction*>::iterator it;
201 <            for (it = interactions_[key].begin();
202 <                 it != interactions_[key].end(); ++it) {
201 >            for (it = interactions_[atid1][atid2].begin();
202 >                 it != interactions_[atid1][atid2].end(); ++it) {
203                InteractionFamily ifam = (*it)->getFamily();
204                if (ifam == VANDERWAALS_FAMILY) {
205 <                interactions_[key].erase(*it);
206 <                // work on iHash here;
205 >                interactions_[atid1][atid2].erase(*it);
206 >                iHash_[atid1][atid2] ^= (*it)->getHash();
207                }
208              }
209 <            interactions_[key].insert(lj_);
210 <            iHash_[key] |= LJ_PAIR;
209 >            interactions_[atid1][atid2].insert(lj_);
210 >            iHash_[atid1][atid2] |= LJ_PAIR;
211              vdwExplicit = true;
212            }
213            
# Line 199 | Line 225 | namespace OpenMD {
225              // We found an explicit Morse interaction.  
226              // override all other vdw entries for this pair of atom types:
227              set<NonBondedInteraction*>::iterator it;
228 <            for (it = interactions_[key].begin();
229 <                 it != interactions_[key].end(); ++it) {
228 >            for (it = interactions_[atid1][atid2].begin();
229 >                 it != interactions_[atid1][atid2].end(); ++it) {
230                InteractionFamily ifam = (*it)->getFamily();
231                if (ifam == VANDERWAALS_FAMILY) {
232 <                interactions_[key].erase(*it);
233 <                // work on iHash here;
232 >                interactions_[atid1][atid2].erase(*it);
233 >                iHash_[atid1][atid2] ^= (*it)->getHash();
234                }
235              }
236 <            interactions_[key].insert(morse_);
237 <            iHash_[key] |= MORSE_PAIR;
236 >            interactions_[atid1][atid2].insert(morse_);
237 >            iHash_[atid1][atid2] |= MORSE_PAIR;
238              vdwExplicit = true;
239            }
240  
# Line 226 | Line 252 | namespace OpenMD {
252              // We found an explicit RepulsivePower interaction.  
253              // override all other vdw entries for this pair of atom types:
254              set<NonBondedInteraction*>::iterator it;
255 <            for (it = interactions_[key].begin();
256 <                 it != interactions_[key].end(); ++it) {
255 >            for (it = interactions_[atid1][atid2].begin();
256 >                 it != interactions_[atid1][atid2].end(); ++it) {
257                InteractionFamily ifam = (*it)->getFamily();
258                if (ifam == VANDERWAALS_FAMILY) {
259 <                interactions_[key].erase(*it);
260 <                // work on iHash here;
259 >                interactions_[atid1][atid2].erase(*it);
260 >                iHash_[atid1][atid2] ^= (*it)->getHash();
261                }
262              }
263 <            interactions_[key].insert(repulsivePower_);
264 <            iHash_[key] |= REPULSIVEPOWER_PAIR;
263 >            interactions_[atid1][atid2].insert(repulsivePower_);
264 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
265              vdwExplicit = true;
266            }
267            
# Line 244 | Line 270 | namespace OpenMD {
270              // We found an explicit EAM interaction.  
271              // override all other metallic entries for this pair of atom types:
272              set<NonBondedInteraction*>::iterator it;
273 <            for (it = interactions_[key].begin();
274 <                 it != interactions_[key].end(); ++it) {
273 >            for (it = interactions_[atid1][atid2].begin();
274 >                 it != interactions_[atid1][atid2].end(); ++it) {
275                InteractionFamily ifam = (*it)->getFamily();
276                if (ifam == METALLIC_FAMILY) {
277 <                interactions_[key].erase(*it);
278 <                // work on iHash here;
277 >                interactions_[atid1][atid2].erase(*it);
278 >                iHash_[atid1][atid2] ^= (*it)->getHash();
279                }
280              }
281 <            interactions_[key].insert(eam_);
282 <            iHash_[key] |= EAM_PAIR;
281 >            interactions_[atid1][atid2].insert(eam_);
282 >            iHash_[atid1][atid2] |= EAM_PAIR;
283              metExplicit = true;
284            }
285            
# Line 271 | Line 297 | namespace OpenMD {
297              // We found an explicit Sutton-Chen interaction.  
298              // override all other metallic entries for this pair of atom types:
299              set<NonBondedInteraction*>::iterator it;
300 <            for (it = interactions_[key].begin();
301 <                 it != interactions_[key].end(); ++it) {
300 >            for (it = interactions_[atid1][atid2].begin();
301 >                 it != interactions_[atid1][atid2].end(); ++it) {
302                InteractionFamily ifam = (*it)->getFamily();
303                if (ifam == METALLIC_FAMILY) {
304 <                interactions_[key].erase(*it);
305 <                // work on iHash here;
304 >                interactions_[atid1][atid2].erase(*it);
305 >                iHash_[atid1][atid2] ^= (*it)->getHash();
306                }
307              }
308 <            interactions_[key].insert(sc_);
309 <            iHash_[key] |= SC_PAIR;
308 >            interactions_[atid1][atid2].insert(sc_);
309 >            iHash_[atid1][atid2] |= SC_PAIR;
310              metExplicit = true;
311            }
312            
# Line 298 | Line 324 | namespace OpenMD {
324              // We found an explicit MAW interaction.  
325              // override all other vdw entries for this pair of atom types:
326              set<NonBondedInteraction*>::iterator it;
327 <            for (it = interactions_[key].begin();
328 <                 it != interactions_[key].end(); ++it) {
327 >            for (it = interactions_[atid1][atid2].begin();
328 >                 it != interactions_[atid1][atid2].end(); ++it) {
329                InteractionFamily ifam = (*it)->getFamily();
330                if (ifam == VANDERWAALS_FAMILY) {
331 <                interactions_[key].erase(*it);
332 <                // work on iHash here;
331 >                interactions_[atid1][atid2].erase(*it);
332 >                iHash_[atid1][atid2] ^= (*it)->getHash();
333                }
334              }
335 <            interactions_[key].insert(maw_);
336 <            iHash_[key] |= MAW_PAIR;
335 >            interactions_[atid1][atid2].insert(maw_);
336 >            iHash_[atid1][atid2] |= MAW_PAIR;
337              vdwExplicit = true;
338            }        
339          }
# Line 323 | Line 349 | namespace OpenMD {
349  
350      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
351        atype1 = (*it);
352 +      atid1 = atype1->getIdent();
353        for (jt = it; jt != simTypes.end(); ++jt) {
354          atype2 = (*jt);
355 <        key = make_pair(atype1, atype2);
355 >        atid1 = atype1->getIdent();
356          
357 <        if (interactions_[key].size() == 0) {
357 >        if (interactions_[atid1][atid2].size() == 0) {
358            sprintf( painCave.errMsg,
359                     "InteractionManager could not find a matching non-bonded\n"
360                     "\tinteraction for atom types %s - %s\n"
# Line 349 | Line 376 | namespace OpenMD {
376      eam_->setCutoffRadius(rcut);
377    }
378  
379 <  void InteractionManager::doPrePair(InteractionData idat){
379 >  void InteractionManager::doPrePair(InteractionData &idat){
380      
381      if (!initialized_) initialize();
382          
383      // excluded interaction, so just return
384      if (idat.excluded) return;
385  
386 <    int& iHash = iHash_[idat.atypes];
386 >    int& iHash = iHash_[idat.atid1][idat.atid2];
387  
388      if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389      if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);
# Line 373 | Line 400 | namespace OpenMD {
400      return;    
401    }
402    
403 <  void InteractionManager::doPreForce(SelfData sdat){
403 >  void InteractionManager::doPreForce(SelfData &sdat){
404  
405      if (!initialized_) initialize();
406      
407 <    // pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
407 >    int& iHash = iHash_[sdat.atid][sdat.atid];
408  
382 –    int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
383 –
409      if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
410      if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);
411  
412      // set<NonBondedInteraction*>::iterator it;
413      
414 <    // for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
414 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
415      //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416      //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417      //   }
# Line 395 | Line 420 | namespace OpenMD {
420      return;    
421    }
422  
423 <  void InteractionManager::doPair(InteractionData idat){
423 >  void InteractionManager::doPair(InteractionData &idat){
424      
425      if (!initialized_) initialize();
426  
427 <    int& iHash = iHash_[idat.atypes];
427 >    int& iHash = iHash_[idat.atid1][idat.atid2];
428  
429      if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430        
# Line 433 | Line 458 | namespace OpenMD {
458      return;    
459    }
460  
461 <  void InteractionManager::doSelfCorrection(SelfData sdat){
461 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
462  
463      if (!initialized_) initialize();
464      
465 <    int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
465 >    int& iHash = iHash_[sdat.atid][sdat.atid];
466  
467      if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468  
444 –
445 –    // pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
469      // set<NonBondedInteraction*>::iterator it;
470  
471 <    // for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
471 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
472      //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473      //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
474      //   }
# Line 454 | Line 477 | namespace OpenMD {
477      return;    
478    }
479  
480 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
481 +    if (!initialized_) initialize();
482 +    electrostatic_->ReciprocalSpaceSum(pot);
483 +  }
484 +
485    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
486      if (!initialized_) initialize();
487  
488      AtomType* atype = typeMap_[*atid];
489  
462 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
490      set<NonBondedInteraction*>::iterator it;
491      RealType cutoff = 0.0;
492      
493 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
494 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
493 >    for (it = interactions_[*atid][*atid].begin();
494 >         it != interactions_[*atid][*atid].end();
495 >         ++it)
496 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
497      return cutoff;    
498    }
499  
500    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
501      if (!initialized_) initialize();
502      
503 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
503 >    int atid = atype->getIdent();
504 >
505      set<NonBondedInteraction*>::iterator it;
506      RealType cutoff = 0.0;
507      
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
509 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
508 >    for (it = interactions_[atid][atid].begin();
509 >         it != interactions_[atid][atid].end(); ++it)
510 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
511      return cutoff;    
512    }
513   } //end namespace OpenMD

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