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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1755 by gezelter, Thu Jun 14 01:58:35 2012 UTC

# Line 36 | Line 36
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).                        
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 "nonbonded/InteractionManager.hpp"
# Line 51 | Line 52 | namespace OpenMD {
52      gb_ = new GB();
53      sticky_ = new Sticky();
54      morse_ = new Morse();
55 +    repulsivePower_ = new RepulsivePower();
56      eam_ = new EAM();
57      sc_ = new SC();
58      electrostatic_ = new Electrostatic();
# Line 58 | Line 60 | namespace OpenMD {
60    }
61  
62    void InteractionManager::initialize() {
63 <    
63 >
64 >    if (initialized_) return;
65 >
66      ForceField* forceField_ = info_->getForceField();
67      
68      lj_->setForceField(forceField_);
# Line 67 | Line 71 | namespace OpenMD {
71      eam_->setForceField(forceField_);
72      sc_->setForceField(forceField_);
73      morse_->setForceField(forceField_);
74 +    electrostatic_->setSimInfo(info_);
75      electrostatic_->setForceField(forceField_);
76      maw_->setForceField(forceField_);
77 +    repulsivePower_->setForceField(forceField_);
78  
79      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
80      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
# Line 81 | Line 87 | namespace OpenMD {
87           atype1 = atomTypes->nextType(i1)) {
88        
89        // add it to the map:
84 –      AtomTypeProperties atp = atype1->getATP();    
90        
91        pair<map<int,AtomType*>::iterator,bool> ret;    
92 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
92 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
93        if (ret.second == false) {
94          sprintf( painCave.errMsg,
95                   "InteractionManager already had a previous entry with ident %d\n",
96 <                 atp.ident);
96 >                 atype1->getIdent());
97          painCave.severity = OPENMD_INFO;
98          painCave.isFatal = 0;
99          simError();                
# Line 175 | Line 180 | namespace OpenMD {
180                if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
181              }
182              interactions_[key].insert(morse_);
183 +            vdwExplicit = true;
184 +          }
185 +
186 +          if (nbiType->isRepulsivePower()) {
187 +            if (vdwExplicit) {
188 +              sprintf( painCave.errMsg,
189 +                       "InteractionManager::initialize found more than one "
190 +                       "explicit \n"
191 +                       "\tvan der Waals interaction for atom types %s - %s\n",
192 +                       atype1->getName().c_str(), atype2->getName().c_str());
193 +              painCave.severity = OPENMD_ERROR;
194 +              painCave.isFatal = 1;
195 +              simError();
196 +            }
197 +            // We found an explicit RepulsivePower interaction.  
198 +            // override all other vdw entries for this pair of atom types:
199 +            set<NonBondedInteraction*>::iterator it;
200 +            for (it = interactions_[key].begin();
201 +                 it != interactions_[key].end(); ++it) {
202 +              InteractionFamily ifam = (*it)->getFamily();
203 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 +            }
205 +            interactions_[key].insert(repulsivePower_);
206              vdwExplicit = true;
207            }
208            
209 +          
210            if (nbiType->isEAM()) {
211              // We found an explicit EAM interaction.  
212              // override all other metallic entries for this pair of atom types:
# Line 241 | Line 270 | namespace OpenMD {
270      }
271      
272      
273 <    // make sure every pair of atom types in this simulation has a
274 <    // non-bonded interaction:
273 >    // Make sure every pair of atom types in this simulation has a
274 >    // non-bonded interaction.  If not, just inform the user.
275  
276      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
277      set<AtomType*>::iterator it, jt;
278 +
279      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
280        atype1 = (*it);
281 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
281 >      for (jt = it; jt != simTypes.end(); ++jt) {
282          atype2 = (*jt);
283          key = make_pair(atype1, atype2);
284          
285          if (interactions_[key].size() == 0) {
286            sprintf( painCave.errMsg,
287 <                   "InteractionManager unable to find an appropriate non-bonded\n"
288 <                   "\tinteraction for atom types %s - %s\n",
287 >                   "InteractionManager could not find a matching non-bonded\n"
288 >                   "\tinteraction for atom types %s - %s\n"
289 >                   "\tProceeding without this interaction.\n",
290                     atype1->getName().c_str(), atype2->getName().c_str());
291            painCave.severity = OPENMD_INFO;
292 <          painCave.isFatal = 1;
292 >          painCave.isFatal = 0;
293            simError();
294          }
295        }
# Line 266 | Line 297 | namespace OpenMD {
297  
298      initialized_ = true;
299    }
300 +
301 +  void InteractionManager::setCutoffRadius(RealType rcut) {
302 +    
303 +    electrostatic_->setCutoffRadius(rcut);
304 +    eam_->setCutoffRadius(rcut);
305 +  }
306 +
307 +  void InteractionManager::setSwitchingRadius(RealType rswitch) {
308 +    electrostatic_->setSwitchingRadius(rswitch);
309 +  }
310    
311    void InteractionManager::doPrePair(InteractionData idat){
312      
313      if (!initialized_) initialize();
314          
315 +    // excluded interaction, so just return
316 +    if (idat.excluded) return;
317 +
318      set<NonBondedInteraction*>::iterator it;
319  
320      for (it = interactions_[ idat.atypes ].begin();
# Line 302 | Line 346 | namespace OpenMD {
346    void InteractionManager::doPair(InteractionData idat){
347      
348      if (!initialized_) initialize();
349 <  
349 >
350      set<NonBondedInteraction*>::iterator it;
351  
352      for (it = interactions_[ idat.atypes ].begin();
353 <         it != interactions_[ idat.atypes ].end(); ++it)
310 <      (*it)->calcForce(idat);
311 <    
312 <    return;    
313 <  }
353 >         it != interactions_[ idat.atypes ].end(); ++it) {
354  
355 <  void InteractionManager::doSkipCorrection(InteractionData idat){
355 >      // electrostatics still has to worry about indirect
356 >      // contributions from excluded pairs of atoms:
357  
358 <    if (!initialized_) initialize();  
359 <    
319 <    set<NonBondedInteraction*>::iterator it;
320 <
321 <    for (it = interactions_[ idat.atypes ].begin();
322 <         it != interactions_[ idat.atypes ].end(); ++it){
323 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
324 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
358 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
359 >        (*it)->calcForce(idat);
360        }
361      }
362      
# Line 346 | Line 381 | namespace OpenMD {
381  
382    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
383      if (!initialized_) initialize();
384 <    
384 >
385      AtomType* atype = typeMap_[*atid];
386  
387      pair<AtomType*, AtomType*> key = make_pair(atype, atype);

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