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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 1710 by gezelter, Fri May 18 21:44:02 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 67 | Line 69 | namespace OpenMD {
69      eam_->setForceField(forceField_);
70      sc_->setForceField(forceField_);
71      morse_->setForceField(forceField_);
72 +    electrostatic_->setSimInfo(info_);
73      electrostatic_->setForceField(forceField_);
74      maw_->setForceField(forceField_);
75 +    repulsivePower_->setForceField(forceField_);
76  
77      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
78      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
# Line 81 | Line 85 | namespace OpenMD {
85           atype1 = atomTypes->nextType(i1)) {
86        
87        // add it to the map:
84 –      AtomTypeProperties atp = atype1->getATP();    
88        
89        pair<map<int,AtomType*>::iterator,bool> ret;    
90 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
90 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
91        if (ret.second == false) {
92          sprintf( painCave.errMsg,
93                   "InteractionManager already had a previous entry with ident %d\n",
94 <                 atp.ident);
94 >                 atype1->getIdent());
95          painCave.severity = OPENMD_INFO;
96          painCave.isFatal = 0;
97          simError();                
# Line 175 | Line 178 | namespace OpenMD {
178                if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
179              }
180              interactions_[key].insert(morse_);
181 +            vdwExplicit = true;
182 +          }
183 +
184 +          if (nbiType->isRepulsivePower()) {
185 +            if (vdwExplicit) {
186 +              sprintf( painCave.errMsg,
187 +                       "InteractionManager::initialize found more than one "
188 +                       "explicit \n"
189 +                       "\tvan der Waals interaction for atom types %s - %s\n",
190 +                       atype1->getName().c_str(), atype2->getName().c_str());
191 +              painCave.severity = OPENMD_ERROR;
192 +              painCave.isFatal = 1;
193 +              simError();
194 +            }
195 +            // We found an explicit RepulsivePower interaction.  
196 +            // override all other vdw entries for this pair of atom types:
197 +            set<NonBondedInteraction*>::iterator it;
198 +            for (it = interactions_[key].begin();
199 +                 it != interactions_[key].end(); ++it) {
200 +              InteractionFamily ifam = (*it)->getFamily();
201 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
202 +            }
203 +            interactions_[key].insert(repulsivePower_);
204              vdwExplicit = true;
205            }
206            
207 +          
208            if (nbiType->isEAM()) {
209              // We found an explicit EAM interaction.  
210              // override all other metallic entries for this pair of atom types:
# Line 241 | Line 268 | namespace OpenMD {
268      }
269      
270      
271 <    // make sure every pair of atom types in this simulation has a
272 <    // non-bonded interaction:
271 >    // Make sure every pair of atom types in this simulation has a
272 >    // non-bonded interaction.  If not, just inform the user.
273  
274      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
275      set<AtomType*>::iterator it, jt;
276 +
277      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
278        atype1 = (*it);
279 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
279 >      for (jt = it; jt != simTypes.end(); ++jt) {
280          atype2 = (*jt);
281          key = make_pair(atype1, atype2);
282          
283          if (interactions_[key].size() == 0) {
284            sprintf( painCave.errMsg,
285 <                   "InteractionManager unable to find an appropriate non-bonded\n"
286 <                   "\tinteraction for atom types %s - %s\n",
285 >                   "InteractionManager could not find a matching non-bonded\n"
286 >                   "\tinteraction for atom types %s - %s\n"
287 >                   "\tProceeding without this interaction.\n",
288                     atype1->getName().c_str(), atype2->getName().c_str());
289            painCave.severity = OPENMD_INFO;
290 <          painCave.isFatal = 1;
290 >          painCave.isFatal = 0;
291            simError();
292          }
293        }
# Line 266 | Line 295 | namespace OpenMD {
295  
296      initialized_ = true;
297    }
298 +
299 +  void InteractionManager::setCutoffRadius(RealType rcut) {
300 +    
301 +    electrostatic_->setCutoffRadius(rcut);
302 +    eam_->setCutoffRadius(rcut);
303 +  }
304 +
305 +  void InteractionManager::setSwitchingRadius(RealType rswitch) {
306 +    electrostatic_->setSwitchingRadius(rswitch);
307 +  }
308    
309    void InteractionManager::doPrePair(InteractionData idat){
310      
311      if (!initialized_) initialize();
312          
313 +    // excluded interaction, so just return
314 +    if (idat.excluded) return;
315 +
316      set<NonBondedInteraction*>::iterator it;
317  
318      for (it = interactions_[ idat.atypes ].begin();
# Line 302 | Line 344 | namespace OpenMD {
344    void InteractionManager::doPair(InteractionData idat){
345      
346      if (!initialized_) initialize();
347 <  
347 >
348      set<NonBondedInteraction*>::iterator it;
349  
350      for (it = interactions_[ idat.atypes ].begin();
351 <         it != interactions_[ idat.atypes ].end(); ++it)
310 <      (*it)->calcForce(idat);
311 <    
312 <    return;    
313 <  }
351 >         it != interactions_[ idat.atypes ].end(); ++it) {
352  
353 <  void InteractionManager::doSkipCorrection(InteractionData idat){
353 >      // electrostatics still has to worry about indirect
354 >      // contributions from excluded pairs of atoms:
355  
356 <    if (!initialized_) initialize();  
357 <    
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);
356 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
357 >        (*it)->calcForce(idat);
358        }
359      }
360      

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