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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 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).          
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   */
# Line 59 | Line 59 | namespace OpenMD {
59      maw_ = new MAW();
60    }
61  
62 +  InteractionManager::~InteractionManager() {
63 +    delete lj_;
64 +    delete gb_;
65 +    delete sticky_;
66 +    delete morse_;
67 +    delete repulsivePower_;
68 +    delete eam_;
69 +    delete sc_;
70 +    delete electrostatic_;
71 +    delete maw_;
72 +  }
73 +
74    void InteractionManager::initialize() {
75 <    
75 >
76 >    if (initialized_) return;
77 >
78      ForceField* forceField_ = info_->getForceField();
79      
80      lj_->setForceField(forceField_);
# Line 75 | 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;
99 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
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 103 | 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 +        iHash_[atid1][atid2] = 0;
152          
110 –        bool vdwExplicit = false;
111 –        bool metExplicit = false;
112 –        bool hbExplicit = false;
113 –                      
114 –        key = make_pair(atype1, atype2);
115 –        
153          if (atype1->isLennardJones() && atype2->isLennardJones()) {
154 <          interactions_[key].insert(lj_);
154 >          interactions_[atid1][atid2].insert(lj_);
155 >          iHash_[atid1][atid2] |= LJ_PAIR;
156          }
157          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158 <          interactions_[key].insert(electrostatic_);
158 >          interactions_[atid1][atid2].insert(electrostatic_);
159 >          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
160          }
161          if (atype1->isSticky() && atype2->isSticky() ) {
162 <          interactions_[key].insert(sticky_);
162 >          interactions_[atid1][atid2].insert(sticky_);
163 >          iHash_[atid1][atid2] |= STICKY_PAIR;
164          }
165          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166 <          interactions_[key].insert(sticky_);
166 >          interactions_[atid1][atid2].insert(sticky_);
167 >          iHash_[atid1][atid2] |= STICKY_PAIR;
168          }
169          if (atype1->isEAM() && atype2->isEAM() ) {
170 <          interactions_[key].insert(eam_);
170 >          interactions_[atid1][atid2].insert(eam_);
171 >          iHash_[atid1][atid2] |= EAM_PAIR;
172          }
173          if (atype1->isSC() && atype2->isSC() ) {
174 <          interactions_[key].insert(sc_);
174 >          interactions_[atid1][atid2].insert(sc_);
175 >          iHash_[atid1][atid2] |= SC_PAIR;
176          }
177          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178 <          interactions_[key].insert(gb_);
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_);
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 145 | Line 190 | namespace OpenMD {
190          
191          if (nbiType != NULL) {
192  
193 +          bool vdwExplicit = false;
194 +          bool metExplicit = false;
195 +          // bool hbExplicit = false;
196 +
197            if (nbiType->isLennardJones()) {
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) interactions_[key].erase(*it);
204 >              if (ifam == VANDERWAALS_FAMILY) {
205 >                interactions_[atid1][atid2].erase(*it);
206 >                iHash_[atid1][atid2] ^= (*it)->getHash();
207 >              }
208              }
209 <            interactions_[key].insert(lj_);
209 >            interactions_[atid1][atid2].insert(lj_);
210 >            iHash_[atid1][atid2] |= LJ_PAIR;
211              vdwExplicit = true;
212            }
213            
# Line 172 | 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) interactions_[key].erase(*it);
231 >              if (ifam == VANDERWAALS_FAMILY) {
232 >                interactions_[atid1][atid2].erase(*it);
233 >                iHash_[atid1][atid2] ^= (*it)->getHash();
234 >              }
235              }
236 <            interactions_[key].insert(morse_);
236 >            interactions_[atid1][atid2].insert(morse_);
237 >            iHash_[atid1][atid2] |= MORSE_PAIR;
238              vdwExplicit = true;
239            }
240  
# Line 195 | 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) interactions_[key].erase(*it);
258 >              if (ifam == VANDERWAALS_FAMILY) {
259 >                interactions_[atid1][atid2].erase(*it);
260 >                iHash_[atid1][atid2] ^= (*it)->getHash();
261 >              }
262              }
263 <            interactions_[key].insert(repulsivePower_);
263 >            interactions_[atid1][atid2].insert(repulsivePower_);
264 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
265              vdwExplicit = true;
266            }
267            
# Line 209 | 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) interactions_[key].erase(*it);
276 >              if (ifam == METALLIC_FAMILY) {
277 >                interactions_[atid1][atid2].erase(*it);
278 >                iHash_[atid1][atid2] ^= (*it)->getHash();
279 >              }
280              }
281 <            interactions_[key].insert(eam_);
281 >            interactions_[atid1][atid2].insert(eam_);
282 >            iHash_[atid1][atid2] |= EAM_PAIR;
283              metExplicit = true;
284            }
285            
# Line 232 | 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) interactions_[key].erase(*it);
303 >              if (ifam == METALLIC_FAMILY) {
304 >                interactions_[atid1][atid2].erase(*it);
305 >                iHash_[atid1][atid2] ^= (*it)->getHash();
306 >              }
307              }
308 <            interactions_[key].insert(sc_);
308 >            interactions_[atid1][atid2].insert(sc_);
309 >            iHash_[atid1][atid2] |= SC_PAIR;
310              metExplicit = true;
311            }
312            
# Line 255 | 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) interactions_[key].erase(*it);
330 >              if (ifam == VANDERWAALS_FAMILY) {
331 >                interactions_[atid1][atid2].erase(*it);
332 >                iHash_[atid1][atid2] ^= (*it)->getHash();
333 >              }
334              }
335 <            interactions_[key].insert(maw_);
335 >            interactions_[atid1][atid2].insert(maw_);
336 >            iHash_[atid1][atid2] |= MAW_PAIR;
337              vdwExplicit = true;
338            }        
339          }
# Line 276 | 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 302 | Line 376 | namespace OpenMD {
376      eam_->setCutoffRadius(rcut);
377    }
378  
379 <  void InteractionManager::setSwitchingRadius(RealType rswitch) {
306 <    electrostatic_->setSwitchingRadius(rswitch);
307 <  }
308 <  
309 <  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 <    set<NonBondedInteraction*>::iterator it;
386 >    int& iHash = iHash_[idat.atid1][idat.atid2];
387  
388 <    for (it = interactions_[ idat.atypes ].begin();
389 <         it != interactions_[ idat.atypes ].end(); ++it){
390 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
391 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
392 <      }
393 <    }
388 >    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389 >    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);
390 >
391 >    // set<NonBondedInteraction*>::iterator it;
392 >
393 >    // for (it = interactions_[ idat.atypes ].begin();
394 >    //      it != interactions_[ idat.atypes ].end(); ++it){
395 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
396 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
397 >    //   }
398 >    // }
399      
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);
408 <    set<NonBondedInteraction*>::iterator it;
407 >    int& iHash = iHash_[sdat.atid][sdat.atid];
408 >
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){
415 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
416 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417 <      }
418 <    }
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 >    //   }
418 >    // }
419      
420      return;    
421    }
422  
423 <  void InteractionManager::doPair(InteractionData idat){
423 >  void InteractionManager::doPair(InteractionData &idat){
424      
425      if (!initialized_) initialize();
426  
427 <    set<NonBondedInteraction*>::iterator it;
427 >    int& iHash = iHash_[idat.atid1][idat.atid2];
428  
429 <    for (it = interactions_[ idat.atypes ].begin();
430 <         it != interactions_[ idat.atypes ].end(); ++it) {
429 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430 >      
431 >    // electrostatics still has to worry about indirect
432 >    // contributions from excluded pairs of atoms, but nothing else does:
433  
434 <      // electrostatics still has to worry about indirect
354 <      // contributions from excluded pairs of atoms:
434 >    if (idat.excluded) return;
435  
436 <      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
437 <        (*it)->calcForce(idat);
438 <      }
439 <    }
436 >    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
437 >    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
438 >    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
439 >    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
440 >    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
441 >    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
442 >    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
443 >    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);
444 >
445 >    // set<NonBondedInteraction*>::iterator it;
446 >
447 >    // for (it = interactions_[ idat.atypes ].begin();
448 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
449 >
450 >    //   // electrostatics still has to worry about indirect
451 >    //   // contributions from excluded pairs of atoms:
452 >
453 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
454 >    //     (*it)->calcForce(idat);
455 >    //   }
456 >    // }
457      
458      return;    
459    }
460  
461 <  void InteractionManager::doSelfCorrection(SelfData sdat){
461 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
462  
463      if (!initialized_) initialize();
464      
465 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
369 <    set<NonBondedInteraction*>::iterator it;
465 >    int& iHash = iHash_[sdat.atid][sdat.atid];
466  
467 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
468 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
469 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
470 <      }
471 <    }
467 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468 >
469 >    // set<NonBondedInteraction*>::iterator it;
470 >
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 >    //   }
475 >    // }
476        
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 <    
487 >
488      AtomType* atype = typeMap_[*atid];
489  
385 –    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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