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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1586 by gezelter, Tue Jun 21 06:34:35 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 70 | Line 72 | namespace OpenMD {
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 82 | Line 85 | namespace OpenMD {
85           atype1 = atomTypes->nextType(i1)) {
86        
87        // add it to the map:
85 –      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 178 | Line 180 | namespace OpenMD {
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 271 | Line 297 | namespace OpenMD {
297    }
298  
299    void InteractionManager::setCutoffRadius(RealType rcut) {
300 +    
301      electrostatic_->setCutoffRadius(rcut);
302      eam_->setCutoffRadius(rcut);
303    }
# Line 283 | Line 310 | namespace OpenMD {
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 314 | 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)
322 <      (*it)->calcForce(idat);
323 <    
324 <    return;    
325 <  }
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 <
331 <    set<NonBondedInteraction*>::iterator it;
332 <
333 <    for (it = interactions_[ idat.atypes ].begin();
334 <         it != interactions_[ idat.atypes ].end(); ++it){
335 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
336 <        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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