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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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Comparing:
branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 1793 by gezelter, Fri Aug 31 21:16:10 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 70 | Line 74 | namespace OpenMD {
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 82 | Line 87 | namespace OpenMD {
87           atype1 = atomTypes->nextType(i1)) {
88        
89        // add it to the map:
85 –      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 107 | Line 111 | namespace OpenMD {
111          
112          bool vdwExplicit = false;
113          bool metExplicit = false;
110 –        bool hbExplicit = false;
114                        
115          key = make_pair(atype1, atype2);
116          
# Line 178 | Line 181 | namespace OpenMD {
181              interactions_[key].insert(morse_);
182              vdwExplicit = true;
183            }
184 +
185 +          if (nbiType->isRepulsivePower()) {
186 +            if (vdwExplicit) {
187 +              sprintf( painCave.errMsg,
188 +                       "InteractionManager::initialize found more than one "
189 +                       "explicit \n"
190 +                       "\tvan der Waals interaction for atom types %s - %s\n",
191 +                       atype1->getName().c_str(), atype2->getName().c_str());
192 +              painCave.severity = OPENMD_ERROR;
193 +              painCave.isFatal = 1;
194 +              simError();
195 +            }
196 +            // We found an explicit RepulsivePower interaction.  
197 +            // override all other vdw entries for this pair of atom types:
198 +            set<NonBondedInteraction*>::iterator it;
199 +            for (it = interactions_[key].begin();
200 +                 it != interactions_[key].end(); ++it) {
201 +              InteractionFamily ifam = (*it)->getFamily();
202 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
203 +            }
204 +            interactions_[key].insert(repulsivePower_);
205 +            vdwExplicit = true;
206 +          }
207            
208 +          
209            if (nbiType->isEAM()) {
210              // We found an explicit EAM interaction.  
211              // override all other metallic entries for this pair of atom types:
# Line 353 | Line 380 | namespace OpenMD {
380  
381    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
382      if (!initialized_) initialize();
383 <    
383 >
384      AtomType* atype = typeMap_[*atid];
385  
386      pair<AtomType*, AtomType*> key = make_pair(atype, atype);

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