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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 1927 by gezelter, Wed Aug 14 20:19:19 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 >          // Pairs of fluctuating density EAM atoms have their
182 >          // interactions handled via the EAM routines.  All other
183 >          // interactions with these atoms are handled via normal
184 >          // electrostatic channels:
185 >          if (!(atype1->isEAM() && atype2->isEAM())) {
186 >            interactions_[atid1][atid2].insert(electrostatic_);
187 >            iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
188 >          }
189          }
190          if (atype1->isSticky() && atype2->isSticky() ) {
191 <          interactions_[key].insert(sticky_);
191 >          interactions_[atid1][atid2].insert(sticky_);
192 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
193          }
194          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
195 <          interactions_[key].insert(sticky_);
195 >          interactions_[atid1][atid2].insert(sticky_);
196 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
197          }
198          if (atype1->isEAM() && atype2->isEAM() ) {
199 <          interactions_[key].insert(eam_);
199 >          interactions_[atid1][atid2].insert(eam_);
200 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
201          }
202          if (atype1->isSC() && atype2->isSC() ) {
203 <          interactions_[key].insert(sc_);
203 >          interactions_[atid1][atid2].insert(sc_);
204 >          iHash_[atid1][atid2] |= SC_INTERACTION;
205          }
206          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
207 <          interactions_[key].insert(gb_);
207 >          interactions_[atid1][atid2].insert(gb_);
208 >          iHash_[atid1][atid2] |= GB_INTERACTION;
209          }
210          if ((atype1->isGayBerne() && atype2->isLennardJones())
211              || (atype1->isLennardJones() && atype2->isGayBerne())) {
212 <          interactions_[key].insert(gb_);
212 >          interactions_[atid1][atid2].insert(gb_);
213 >          iHash_[atid1][atid2] |= GB_INTERACTION;
214          }
215          
216          // look for an explicitly-set non-bonded interaction type using the
# Line 145 | Line 219 | namespace OpenMD {
219          
220          if (nbiType != NULL) {
221  
222 +          bool vdwExplicit = false;
223 +          bool metExplicit = false;
224 +          // bool hbExplicit = false;
225 +
226            if (nbiType->isLennardJones()) {
227              // We found an explicit Lennard-Jones interaction.  
228              // override all other vdw entries for this pair of atom types:
229              set<NonBondedInteraction*>::iterator it;
230 <            for (it = interactions_[key].begin();
231 <                 it != interactions_[key].end(); ++it) {
230 >            for (it = interactions_[atid1][atid2].begin();
231 >                 it != interactions_[atid1][atid2].end(); ++it) {
232                InteractionFamily ifam = (*it)->getFamily();
233 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
233 >              if (ifam == VANDERWAALS_FAMILY) {
234 >                interactions_[atid1][atid2].erase(*it);
235 >                iHash_[atid1][atid2] ^= (*it)->getHash();
236 >              }
237              }
238 <            interactions_[key].insert(lj_);
238 >            interactions_[atid1][atid2].insert(lj_);
239 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
240              vdwExplicit = true;
241            }
242            
# Line 172 | Line 254 | namespace OpenMD {
254              // We found an explicit Morse interaction.  
255              // override all other vdw entries for this pair of atom types:
256              set<NonBondedInteraction*>::iterator it;
257 <            for (it = interactions_[key].begin();
258 <                 it != interactions_[key].end(); ++it) {
257 >            for (it = interactions_[atid1][atid2].begin();
258 >                 it != interactions_[atid1][atid2].end(); ++it) {
259                InteractionFamily ifam = (*it)->getFamily();
260 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
260 >              if (ifam == VANDERWAALS_FAMILY) {
261 >                interactions_[atid1][atid2].erase(*it);
262 >                iHash_[atid1][atid2] ^= (*it)->getHash();
263 >              }
264              }
265 <            interactions_[key].insert(morse_);
265 >            interactions_[atid1][atid2].insert(morse_);
266 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
267              vdwExplicit = true;
268            }
269  
# Line 195 | Line 281 | namespace OpenMD {
281              // We found an explicit RepulsivePower interaction.  
282              // override all other vdw entries for this pair of atom types:
283              set<NonBondedInteraction*>::iterator it;
284 <            for (it = interactions_[key].begin();
285 <                 it != interactions_[key].end(); ++it) {
284 >            for (it = interactions_[atid1][atid2].begin();
285 >                 it != interactions_[atid1][atid2].end(); ++it) {
286                InteractionFamily ifam = (*it)->getFamily();
287 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
287 >              if (ifam == VANDERWAALS_FAMILY) {
288 >                interactions_[atid1][atid2].erase(*it);
289 >                iHash_[atid1][atid2] ^= (*it)->getHash();
290 >              }
291              }
292 <            interactions_[key].insert(repulsivePower_);
292 >            interactions_[atid1][atid2].insert(repulsivePower_);
293 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
294              vdwExplicit = true;
295            }
296            
# Line 209 | Line 299 | namespace OpenMD {
299              // We found an explicit EAM interaction.  
300              // override all other metallic entries for this pair of atom types:
301              set<NonBondedInteraction*>::iterator it;
302 <            for (it = interactions_[key].begin();
303 <                 it != interactions_[key].end(); ++it) {
302 >            for (it = interactions_[atid1][atid2].begin();
303 >                 it != interactions_[atid1][atid2].end(); ++it) {
304                InteractionFamily ifam = (*it)->getFamily();
305 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
305 >              if (ifam == METALLIC_FAMILY) {
306 >                interactions_[atid1][atid2].erase(*it);
307 >                iHash_[atid1][atid2] ^= (*it)->getHash();
308 >              }
309              }
310 <            interactions_[key].insert(eam_);
310 >            interactions_[atid1][atid2].insert(eam_);
311 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
312              metExplicit = true;
313            }
314            
# Line 232 | Line 326 | namespace OpenMD {
326              // We found an explicit Sutton-Chen interaction.  
327              // override all other metallic entries for this pair of atom types:
328              set<NonBondedInteraction*>::iterator it;
329 <            for (it = interactions_[key].begin();
330 <                 it != interactions_[key].end(); ++it) {
329 >            for (it = interactions_[atid1][atid2].begin();
330 >                 it != interactions_[atid1][atid2].end(); ++it) {
331                InteractionFamily ifam = (*it)->getFamily();
332 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
332 >              if (ifam == METALLIC_FAMILY) {
333 >                interactions_[atid1][atid2].erase(*it);
334 >                iHash_[atid1][atid2] ^= (*it)->getHash();
335 >              }
336              }
337 <            interactions_[key].insert(sc_);
337 >            interactions_[atid1][atid2].insert(sc_);
338 >            iHash_[atid1][atid2] |= SC_INTERACTION;
339              metExplicit = true;
340            }
341            
# Line 255 | Line 353 | namespace OpenMD {
353              // We found an explicit MAW interaction.  
354              // override all other vdw entries for this pair of atom types:
355              set<NonBondedInteraction*>::iterator it;
356 <            for (it = interactions_[key].begin();
357 <                 it != interactions_[key].end(); ++it) {
356 >            for (it = interactions_[atid1][atid2].begin();
357 >                 it != interactions_[atid1][atid2].end(); ++it) {
358                InteractionFamily ifam = (*it)->getFamily();
359 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
359 >              if (ifam == VANDERWAALS_FAMILY) {
360 >                interactions_[atid1][atid2].erase(*it);
361 >                iHash_[atid1][atid2] ^= (*it)->getHash();
362 >              }
363              }
364 <            interactions_[key].insert(maw_);
364 >            interactions_[atid1][atid2].insert(maw_);
365 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
366              vdwExplicit = true;
367            }        
368          }
# Line 276 | Line 378 | namespace OpenMD {
378  
379      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
380        atype1 = (*it);
381 +      atid1 = atype1->getIdent();
382        for (jt = it; jt != simTypes.end(); ++jt) {
383          atype2 = (*jt);
384 <        key = make_pair(atype1, atype2);
384 >        atid1 = atype1->getIdent();
385          
386 <        if (interactions_[key].size() == 0) {
386 >        if (interactions_[atid1][atid2].size() == 0) {
387            sprintf( painCave.errMsg,
388                     "InteractionManager could not find a matching non-bonded\n"
389                     "\tinteraction for atom types %s - %s\n"
# Line 302 | Line 405 | namespace OpenMD {
405      eam_->setCutoffRadius(rcut);
406    }
407  
408 <  void InteractionManager::setSwitchingRadius(RealType rswitch) {
306 <    electrostatic_->setSwitchingRadius(rswitch);
307 <  }
308 <  
309 <  void InteractionManager::doPrePair(InteractionData idat){
408 >  void InteractionManager::doPrePair(InteractionData &idat){
409      
410      if (!initialized_) initialize();
411          
412      // excluded interaction, so just return
413      if (idat.excluded) return;
414  
415 <    set<NonBondedInteraction*>::iterator it;
415 >    int& iHash = iHash_[idat.atid1][idat.atid2];
416  
417 <    for (it = interactions_[ idat.atypes ].begin();
418 <         it != interactions_[ idat.atypes ].end(); ++it){
419 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
420 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
421 <      }
422 <    }
417 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
418 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
419 >
420 >    // set<NonBondedInteraction*>::iterator it;
421 >
422 >    // for (it = interactions_[ idat.atypes ].begin();
423 >    //      it != interactions_[ idat.atypes ].end(); ++it){
424 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
425 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
426 >    //   }
427 >    // }
428      
429      return;    
430    }
431    
432 <  void InteractionManager::doPreForce(SelfData sdat){
432 >  void InteractionManager::doPreForce(SelfData &sdat){
433  
434      if (!initialized_) initialize();
435      
436 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
437 <    set<NonBondedInteraction*>::iterator it;
436 >    int& sHash = sHash_[sdat.atid];
437 >
438 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
439 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
440 >
441 >    // set<NonBondedInteraction*>::iterator it;
442      
443 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
444 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
445 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
446 <      }
447 <    }
443 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
444 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
445 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
446 >    //   }
447 >    // }
448      
449      return;    
450    }
451  
452 <  void InteractionManager::doPair(InteractionData idat){
452 >  void InteractionManager::doPair(InteractionData &idat){
453      
454      if (!initialized_) initialize();
455  
456 <    set<NonBondedInteraction*>::iterator it;
456 >    int& iHash = iHash_[idat.atid1][idat.atid2];
457  
458 <    for (it = interactions_[ idat.atypes ].begin();
459 <         it != interactions_[ idat.atypes ].end(); ++it) {
458 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
459 >      
460 >    // electrostatics still has to worry about indirect
461 >    // contributions from excluded pairs of atoms, but nothing else does:
462  
463 <      // electrostatics still has to worry about indirect
354 <      // contributions from excluded pairs of atoms:
463 >    if (idat.excluded) return;
464  
465 <      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
466 <        (*it)->calcForce(idat);
467 <      }
468 <    }
465 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
466 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
467 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
468 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
469 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
470 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
471 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
472 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
473 >
474 >    // set<NonBondedInteraction*>::iterator it;
475 >
476 >    // for (it = interactions_[ idat.atypes ].begin();
477 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
478 >
479 >    //   // electrostatics still has to worry about indirect
480 >    //   // contributions from excluded pairs of atoms:
481 >
482 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
483 >    //     (*it)->calcForce(idat);
484 >    //   }
485 >    // }
486      
487      return;    
488    }
489  
490 <  void InteractionManager::doSelfCorrection(SelfData sdat){
490 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
491  
492      if (!initialized_) initialize();
493      
494 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
369 <    set<NonBondedInteraction*>::iterator it;
494 >    int& sHash = sHash_[sdat.atid];
495  
496 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
497 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
498 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
499 <      }
500 <    }
496 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
497 >
498 >    // set<NonBondedInteraction*>::iterator it;
499 >
500 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
501 >    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
502 >    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
503 >    //   }
504 >    // }
505        
506      return;    
507    }
508  
509 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
510 +    if (!initialized_) initialize();
511 +    electrostatic_->ReciprocalSpaceSum(pot);
512 +  }
513 +
514    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
515      if (!initialized_) initialize();
516 <    
516 >
517      AtomType* atype = typeMap_[*atid];
518  
385 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
519      set<NonBondedInteraction*>::iterator it;
520      RealType cutoff = 0.0;
521      
522 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
523 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
522 >    for (it = interactions_[*atid][*atid].begin();
523 >         it != interactions_[*atid][*atid].end();
524 >         ++it)
525 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
526      return cutoff;    
527    }
528  
529    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
530      if (!initialized_) initialize();
531      
532 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
532 >    int atid = atype->getIdent();
533 >
534      set<NonBondedInteraction*>::iterator it;
535      RealType cutoff = 0.0;
536      
537 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
538 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
537 >    for (it = interactions_[atid][atid].begin();
538 >         it != interactions_[atid][atid].end(); ++it)
539 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
540      return cutoff;    
541    }
542   } //end namespace OpenMD

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