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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 176 | Line 179 | namespace OpenMD {
179                if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
180              }
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 271 | Line 298 | namespace OpenMD {
298    }
299  
300    void InteractionManager::setCutoffRadius(RealType rcut) {
301 +    
302      electrostatic_->setCutoffRadius(rcut);
303      eam_->setCutoffRadius(rcut);
304    }
# Line 283 | Line 311 | namespace OpenMD {
311      
312      if (!initialized_) initialize();
313          
314 +    // excluded interaction, so just return
315 +    if (idat.excluded) return;
316 +
317      set<NonBondedInteraction*>::iterator it;
318  
319      for (it = interactions_[ idat.atypes ].begin();
# Line 314 | Line 345 | namespace OpenMD {
345    void InteractionManager::doPair(InteractionData idat){
346      
347      if (!initialized_) initialize();
348 <  
348 >
349      set<NonBondedInteraction*>::iterator it;
350  
351      for (it = interactions_[ idat.atypes ].begin();
352 <         it != interactions_[ idat.atypes ].end(); ++it)
322 <      (*it)->calcForce(idat);
323 <    
324 <    return;    
325 <  }
352 >         it != interactions_[ idat.atypes ].end(); ++it) {
353  
354 <  void InteractionManager::doSkipCorrection(InteractionData idat){
354 >      // electrostatics still has to worry about indirect
355 >      // contributions from excluded pairs of atoms:
356  
357 <    if (!initialized_) initialize();  
358 <
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);
357 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
358 >        (*it)->calcForce(idat);
359        }
360      }
361      

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