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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 1929 by gezelter, Mon Aug 19 13:12:00 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 +    sHash_.resize(nTypes);
94 +    iHash_.resize(nTypes);
95 +    interactions_.resize(nTypes);
96      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
97      AtomType* atype1;
98      AtomType* atype2;
99 <    pair<AtomType*, AtomType*> key;
100 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
99 >    int atid1, atid2;
100 >
101 >    // We only need to worry about the types that are actually in the simulation:
102 >
103 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
104 >
105 >    lj_->setSimulatedAtomTypes(atypes);
106 >    gb_->setSimulatedAtomTypes(atypes);
107 >    sticky_->setSimulatedAtomTypes(atypes);
108 >    eam_->setSimulatedAtomTypes(atypes);
109 >    sc_->setSimulatedAtomTypes(atypes);
110 >    morse_->setSimulatedAtomTypes(atypes);
111 >    electrostatic_->setSimInfo(info_);
112 >    electrostatic_->setSimulatedAtomTypes(atypes);
113 >    maw_->setSimulatedAtomTypes(atypes);
114 >    repulsivePower_->setSimulatedAtomTypes(atypes);
115 >
116 >    set<AtomType*>::iterator at;
117 >
118 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
119      
120 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
121 <         atype1 = atomTypes->nextType(i1)) {
120 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
121 >      //   atype1 = atomTypes->nextType(i1)) {
122        
123 <      // add it to the map:
124 <      
123 >      atype1 = *at;
124 >      atid1 = atype1->getIdent();
125 >      iHash_[atid1].resize(nTypes);
126 >      interactions_[atid1].resize(nTypes);
127 >
128 >      // add it to the map:      
129        pair<map<int,AtomType*>::iterator,bool> ret;    
130 <      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
130 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
131        if (ret.second == false) {
132          sprintf( painCave.errMsg,
133                   "InteractionManager already had a previous entry with ident %d\n",
# Line 97 | Line 137 | namespace OpenMD {
137          simError();                
138        }
139      }
140 <    
140 >
141 >    if (atype1->isLennardJones()) {
142 >      sHash_[atid1] |= LJ_INTERACTION;
143 >    }
144 >    if (atype1->isElectrostatic()) {
145 >      sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
146 >    }
147 >    if (atype1->isSticky()) {
148 >      sHash_[atid1] |= STICKY_INTERACTION;
149 >    }
150 >    if (atype1->isStickyPower()) {
151 >      sHash_[atid1] |= STICKY_INTERACTION;
152 >    }
153 >    if (atype1->isEAM()) {
154 >      sHash_[atid1] |= EAM_INTERACTION;
155 >    }
156 >    if (atype1->isSC()) {
157 >      sHash_[atid1] |= SC_INTERACTION;
158 >    }
159 >    if (atype1->isGayBerne()) {
160 >      sHash_[atid1] |= GB_INTERACTION;
161 >    }
162 >  
163      // Now, iterate over all known types and add to the interaction map:
164      
165      map<int, AtomType*>::iterator it1, it2;
166      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
167        atype1 = (*it1).second;
168 +      atid1 = atype1->getIdent();
169  
170        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
171          atype2 = (*it2).second;
172 +        atid2 = atype2->getIdent();
173 +                              
174 +        iHash_[atid1][atid2] = 0;
175          
110 –        bool vdwExplicit = false;
111 –        bool metExplicit = false;
112 –        bool hbExplicit = false;
113 –                      
114 –        key = make_pair(atype1, atype2);
115 –        
176          if (atype1->isLennardJones() && atype2->isLennardJones()) {
177 <          interactions_[key].insert(lj_);
177 >          interactions_[atid1][atid2].insert(lj_);
178 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
179          }
180          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
181 <          interactions_[key].insert(electrostatic_);
181 >          interactions_[atid1][atid2].insert(electrostatic_);
182 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
183          }
184          if (atype1->isSticky() && atype2->isSticky() ) {
185 <          interactions_[key].insert(sticky_);
185 >          interactions_[atid1][atid2].insert(sticky_);
186 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
187          }
188          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
189 <          interactions_[key].insert(sticky_);
189 >          interactions_[atid1][atid2].insert(sticky_);
190 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
191          }
192          if (atype1->isEAM() && atype2->isEAM() ) {
193 <          interactions_[key].insert(eam_);
193 >          interactions_[atid1][atid2].insert(eam_);
194 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
195          }
196          if (atype1->isSC() && atype2->isSC() ) {
197 <          interactions_[key].insert(sc_);
197 >          interactions_[atid1][atid2].insert(sc_);
198 >          iHash_[atid1][atid2] |= SC_INTERACTION;
199          }
200          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
201 <          interactions_[key].insert(gb_);
201 >          interactions_[atid1][atid2].insert(gb_);
202 >          iHash_[atid1][atid2] |= GB_INTERACTION;
203          }
204          if ((atype1->isGayBerne() && atype2->isLennardJones())
205              || (atype1->isLennardJones() && atype2->isGayBerne())) {
206 <          interactions_[key].insert(gb_);
206 >          interactions_[atid1][atid2].insert(gb_);
207 >          iHash_[atid1][atid2] |= GB_INTERACTION;
208          }
209          
210          // look for an explicitly-set non-bonded interaction type using the
# Line 145 | Line 213 | namespace OpenMD {
213          
214          if (nbiType != NULL) {
215  
216 +          bool vdwExplicit = false;
217 +          bool metExplicit = false;
218 +          // bool hbExplicit = false;
219 +
220            if (nbiType->isLennardJones()) {
221              // We found an explicit Lennard-Jones interaction.  
222              // override all other vdw entries for this pair of atom types:
223              set<NonBondedInteraction*>::iterator it;
224 <            for (it = interactions_[key].begin();
225 <                 it != interactions_[key].end(); ++it) {
224 >            for (it = interactions_[atid1][atid2].begin();
225 >                 it != interactions_[atid1][atid2].end(); ++it) {
226                InteractionFamily ifam = (*it)->getFamily();
227 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
227 >              if (ifam == VANDERWAALS_FAMILY) {
228 >                interactions_[atid1][atid2].erase(*it);
229 >                iHash_[atid1][atid2] ^= (*it)->getHash();
230 >              }
231              }
232 <            interactions_[key].insert(lj_);
232 >            interactions_[atid1][atid2].insert(lj_);
233 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
234              vdwExplicit = true;
235            }
236            
# Line 172 | Line 248 | namespace OpenMD {
248              // We found an explicit Morse interaction.  
249              // override all other vdw entries for this pair of atom types:
250              set<NonBondedInteraction*>::iterator it;
251 <            for (it = interactions_[key].begin();
252 <                 it != interactions_[key].end(); ++it) {
251 >            for (it = interactions_[atid1][atid2].begin();
252 >                 it != interactions_[atid1][atid2].end(); ++it) {
253                InteractionFamily ifam = (*it)->getFamily();
254 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
254 >              if (ifam == VANDERWAALS_FAMILY) {
255 >                interactions_[atid1][atid2].erase(*it);
256 >                iHash_[atid1][atid2] ^= (*it)->getHash();
257 >              }
258              }
259 <            interactions_[key].insert(morse_);
259 >            interactions_[atid1][atid2].insert(morse_);
260 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
261              vdwExplicit = true;
262            }
263  
# Line 195 | Line 275 | namespace OpenMD {
275              // We found an explicit RepulsivePower interaction.  
276              // override all other vdw entries for this pair of atom types:
277              set<NonBondedInteraction*>::iterator it;
278 <            for (it = interactions_[key].begin();
279 <                 it != interactions_[key].end(); ++it) {
278 >            for (it = interactions_[atid1][atid2].begin();
279 >                 it != interactions_[atid1][atid2].end(); ++it) {
280                InteractionFamily ifam = (*it)->getFamily();
281 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
281 >              if (ifam == VANDERWAALS_FAMILY) {
282 >                interactions_[atid1][atid2].erase(*it);
283 >                iHash_[atid1][atid2] ^= (*it)->getHash();
284 >              }
285              }
286 <            interactions_[key].insert(repulsivePower_);
286 >            interactions_[atid1][atid2].insert(repulsivePower_);
287 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
288              vdwExplicit = true;
289            }
290            
# Line 209 | Line 293 | namespace OpenMD {
293              // We found an explicit EAM interaction.  
294              // override all other metallic entries for this pair of atom types:
295              set<NonBondedInteraction*>::iterator it;
296 <            for (it = interactions_[key].begin();
297 <                 it != interactions_[key].end(); ++it) {
296 >            for (it = interactions_[atid1][atid2].begin();
297 >                 it != interactions_[atid1][atid2].end(); ++it) {
298                InteractionFamily ifam = (*it)->getFamily();
299 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
299 >              if (ifam == METALLIC_FAMILY) {
300 >                interactions_[atid1][atid2].erase(*it);
301 >                iHash_[atid1][atid2] ^= (*it)->getHash();
302 >              }
303              }
304 <            interactions_[key].insert(eam_);
304 >            interactions_[atid1][atid2].insert(eam_);
305 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
306              metExplicit = true;
307            }
308            
# Line 232 | Line 320 | namespace OpenMD {
320              // We found an explicit Sutton-Chen interaction.  
321              // override all other metallic entries for this pair of atom types:
322              set<NonBondedInteraction*>::iterator it;
323 <            for (it = interactions_[key].begin();
324 <                 it != interactions_[key].end(); ++it) {
323 >            for (it = interactions_[atid1][atid2].begin();
324 >                 it != interactions_[atid1][atid2].end(); ++it) {
325                InteractionFamily ifam = (*it)->getFamily();
326 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
326 >              if (ifam == METALLIC_FAMILY) {
327 >                interactions_[atid1][atid2].erase(*it);
328 >                iHash_[atid1][atid2] ^= (*it)->getHash();
329 >              }
330              }
331 <            interactions_[key].insert(sc_);
331 >            interactions_[atid1][atid2].insert(sc_);
332 >            iHash_[atid1][atid2] |= SC_INTERACTION;
333              metExplicit = true;
334            }
335            
# Line 255 | Line 347 | namespace OpenMD {
347              // We found an explicit MAW interaction.  
348              // override all other vdw entries for this pair of atom types:
349              set<NonBondedInteraction*>::iterator it;
350 <            for (it = interactions_[key].begin();
351 <                 it != interactions_[key].end(); ++it) {
350 >            for (it = interactions_[atid1][atid2].begin();
351 >                 it != interactions_[atid1][atid2].end(); ++it) {
352                InteractionFamily ifam = (*it)->getFamily();
353 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
353 >              if (ifam == VANDERWAALS_FAMILY) {
354 >                interactions_[atid1][atid2].erase(*it);
355 >                iHash_[atid1][atid2] ^= (*it)->getHash();
356 >              }
357              }
358 <            interactions_[key].insert(maw_);
358 >            interactions_[atid1][atid2].insert(maw_);
359 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
360              vdwExplicit = true;
361            }        
362          }
# Line 276 | Line 372 | namespace OpenMD {
372  
373      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
374        atype1 = (*it);
375 +      atid1 = atype1->getIdent();
376        for (jt = it; jt != simTypes.end(); ++jt) {
377          atype2 = (*jt);
378 <        key = make_pair(atype1, atype2);
378 >        atid1 = atype1->getIdent();
379          
380 <        if (interactions_[key].size() == 0) {
380 >        if (interactions_[atid1][atid2].size() == 0) {
381            sprintf( painCave.errMsg,
382                     "InteractionManager could not find a matching non-bonded\n"
383                     "\tinteraction for atom types %s - %s\n"
# Line 302 | Line 399 | namespace OpenMD {
399      eam_->setCutoffRadius(rcut);
400    }
401  
402 <  void InteractionManager::setSwitchingRadius(RealType rswitch) {
306 <    electrostatic_->setSwitchingRadius(rswitch);
307 <  }
308 <  
309 <  void InteractionManager::doPrePair(InteractionData idat){
402 >  void InteractionManager::doPrePair(InteractionData &idat){
403      
404      if (!initialized_) initialize();
405          
406      // excluded interaction, so just return
407      if (idat.excluded) return;
408  
409 <    set<NonBondedInteraction*>::iterator it;
409 >    int& iHash = iHash_[idat.atid1][idat.atid2];
410  
411 <    for (it = interactions_[ idat.atypes ].begin();
412 <         it != interactions_[ idat.atypes ].end(); ++it){
413 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
414 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
415 <      }
416 <    }
411 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
412 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
413 >
414 >    // set<NonBondedInteraction*>::iterator it;
415 >
416 >    // for (it = interactions_[ idat.atypes ].begin();
417 >    //      it != interactions_[ idat.atypes ].end(); ++it){
418 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
419 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
420 >    //   }
421 >    // }
422      
423      return;    
424    }
425    
426 <  void InteractionManager::doPreForce(SelfData sdat){
426 >  void InteractionManager::doPreForce(SelfData &sdat){
427  
428      if (!initialized_) initialize();
429      
430 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
431 <    set<NonBondedInteraction*>::iterator it;
430 >    int& sHash = sHash_[sdat.atid];
431 >
432 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
433 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
434 >
435 >    // set<NonBondedInteraction*>::iterator it;
436      
437 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
438 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
439 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
440 <      }
441 <    }
437 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
438 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
439 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
440 >    //   }
441 >    // }
442      
443      return;    
444    }
445  
446 <  void InteractionManager::doPair(InteractionData idat){
446 >  void InteractionManager::doPair(InteractionData &idat){
447      
448      if (!initialized_) initialize();
449  
450 <    set<NonBondedInteraction*>::iterator it;
450 >    int& iHash = iHash_[idat.atid1][idat.atid2];
451  
452 <    for (it = interactions_[ idat.atypes ].begin();
453 <         it != interactions_[ idat.atypes ].end(); ++it) {
452 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
453 >      
454 >    // electrostatics still has to worry about indirect
455 >    // contributions from excluded pairs of atoms, but nothing else does:
456  
457 <      // electrostatics still has to worry about indirect
354 <      // contributions from excluded pairs of atoms:
457 >    if (idat.excluded) return;
458  
459 <      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
460 <        (*it)->calcForce(idat);
461 <      }
462 <    }
459 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
460 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
461 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
462 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
463 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
464 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
465 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
466 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
467 >
468 >    // set<NonBondedInteraction*>::iterator it;
469 >
470 >    // for (it = interactions_[ idat.atypes ].begin();
471 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
472 >
473 >    //   // electrostatics still has to worry about indirect
474 >    //   // contributions from excluded pairs of atoms:
475 >
476 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
477 >    //     (*it)->calcForce(idat);
478 >    //   }
479 >    // }
480      
481      return;    
482    }
483  
484 <  void InteractionManager::doSelfCorrection(SelfData sdat){
484 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
485  
486      if (!initialized_) initialize();
487      
488 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
369 <    set<NonBondedInteraction*>::iterator it;
488 >    int& sHash = sHash_[sdat.atid];
489  
490 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
491 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
492 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
493 <      }
494 <    }
490 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
491 >
492 >    // set<NonBondedInteraction*>::iterator it;
493 >
494 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
495 >    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
496 >    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
497 >    //   }
498 >    // }
499        
500      return;    
501    }
502  
503 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
504 +    if (!initialized_) initialize();
505 +    electrostatic_->ReciprocalSpaceSum(pot);
506 +  }
507 +
508    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
509      if (!initialized_) initialize();
510 <    
510 >
511      AtomType* atype = typeMap_[*atid];
512  
385 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
513      set<NonBondedInteraction*>::iterator it;
514      RealType cutoff = 0.0;
515      
516 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
517 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
516 >    for (it = interactions_[*atid][*atid].begin();
517 >         it != interactions_[*atid][*atid].end();
518 >         ++it)
519 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
520      return cutoff;    
521    }
522  
523    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
524      if (!initialized_) initialize();
525      
526 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
526 >    int atid = atype->getIdent();
527 >
528      set<NonBondedInteraction*>::iterator it;
529      RealType cutoff = 0.0;
530      
531 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
532 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
531 >    for (it = interactions_[atid][atid].begin();
532 >         it != interactions_[atid][atid].end(); ++it)
533 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
534      return cutoff;    
535    }
536   } //end namespace OpenMD

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