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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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"
44  
45   namespace OpenMD {
45 –
46 –  bool InteractionManager::initialized_ = false;
47 –  RealType InteractionManager::rCut_ = -1.0;
48 –  RealType InteractionManager::rSwitch_ = -1.0;
49 –  ForceField* InteractionManager::forceField_ = NULL;  
50 –  InteractionManager* InteractionManager::_instance = NULL;
51 –  map<int, AtomType*> InteractionManager::typeMap_;
52 –  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
46  
47 <  LJ* InteractionManager::lj_ = new LJ();
48 <  GB* InteractionManager::gb_ = new GB();
49 <  Sticky* InteractionManager::sticky_ = new Sticky();
50 <  Morse* InteractionManager::morse_ = new Morse();
51 <  EAM* InteractionManager::eam_ = new EAM();
52 <  SC* InteractionManager::sc_ = new SC();
53 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
54 <  MAW* InteractionManager::maw_ = new MAW();
55 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
56 <
57 <  InteractionManager* InteractionManager::Instance() {
58 <    if (!_instance) {
59 <      _instance = new InteractionManager();
67 <    }
68 <    return _instance;
47 >  InteractionManager::InteractionManager() {
48 >
49 >    initialized_ = false;
50 >        
51 >    lj_ = new LJ();
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();
59 >    maw_ = new MAW();
60    }
61  
62 +  InteractionManager::~InteractionManager() {
63 +    delete lj_;
64 +    delete gb_;
65 +    delete sticky_;
66 +    delete morse_;
67 +    delete repulsivePower_;
68 +    delete eam_;
69 +    delete sc_;
70 +    delete electrostatic_;
71 +    delete maw_;
72 +  }
73 +
74    void InteractionManager::initialize() {
75 +
76 +    if (initialized_) return;
77 +
78 +    ForceField* forceField_ = info_->getForceField();
79      
80      lj_->setForceField(forceField_);
81      gb_->setForceField(forceField_);
# Line 76 | Line 83 | namespace OpenMD {
83      eam_->setForceField(forceField_);
84      sc_->setForceField(forceField_);
85      morse_->setForceField(forceField_);
86 +    electrostatic_->setSimInfo(info_);
87      electrostatic_->setForceField(forceField_);
88      maw_->setForceField(forceField_);
89 +    repulsivePower_->setForceField(forceField_);
90  
82 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
83 –    // Force fields can set options on how to scale van der Waals and electrostatic
84 –    // interactions for atoms connected via bonds, bends and torsions
85 –    // in this case the topological distance between atoms is:
86 –    // 0 = the atom itself
87 –    // 1 = bonded together
88 –    // 2 = connected via a bend
89 –    // 3 = connected via a torsion
90 –
91 –    vdwScale_[0] = 0.0;
92 –    vdwScale_[1] = fopts.getvdw12scale();
93 –    vdwScale_[2] = fopts.getvdw13scale();
94 –    vdwScale_[3] = fopts.getvdw14scale();
95 –
96 –    electrostaticScale_[0] = 0.0;
97 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
98 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
99 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();
100 –
91      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92 +    int nTypes = atomTypes->size();
93 +    sHash_.resize(nTypes);
94 +    iHash_.resize(nTypes);
95 +    interactions_.resize(nTypes);
96      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
97      AtomType* atype1;
98      AtomType* atype2;
99 <    pair<AtomType*, AtomType*> key;
100 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
99 >    int atid1, atid2;
100 >
101 >    // We only need to worry about the types that are actually in the simulation:
102 >
103 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
104 >
105 >    lj_->setSimulatedAtomTypes(atypes);
106 >    gb_->setSimulatedAtomTypes(atypes);
107 >    sticky_->setSimulatedAtomTypes(atypes);
108 >    eam_->setSimulatedAtomTypes(atypes);
109 >    sc_->setSimulatedAtomTypes(atypes);
110 >    morse_->setSimulatedAtomTypes(atypes);
111 >    electrostatic_->setSimInfo(info_);
112 >    electrostatic_->setSimulatedAtomTypes(atypes);
113 >    maw_->setSimulatedAtomTypes(atypes);
114 >    repulsivePower_->setSimulatedAtomTypes(atypes);
115 >
116 >    set<AtomType*>::iterator at;
117 >
118 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
119      
120 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
121 <         atype1 = atomTypes->nextType(i1)) {
120 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
121 >      //   atype1 = atomTypes->nextType(i1)) {
122        
123 <      // add it to the map:
124 <      AtomTypeProperties atp = atype1->getATP();    
125 <      
123 >      atype1 = *at;
124 >      atid1 = atype1->getIdent();
125 >      iHash_[atid1].resize(nTypes);
126 >      interactions_[atid1].resize(nTypes);
127 >
128 >      // add it to the map:      
129        pair<map<int,AtomType*>::iterator,bool> ret;    
130 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
130 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
131        if (ret.second == false) {
132          sprintf( painCave.errMsg,
133                   "InteractionManager already had a previous entry with ident %d\n",
134 <                 atp.ident);
134 >                 atype1->getIdent());
135          painCave.severity = OPENMD_INFO;
136          painCave.isFatal = 0;
137          simError();                
138        }
139      }
140 <    
140 >
141 >    if (atype1->isLennardJones()) {
142 >      sHash_[atid1] |= LJ_INTERACTION;
143 >    }
144 >    if (atype1->isElectrostatic()) {
145 >      sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
146 >    }
147 >    if (atype1->isSticky()) {
148 >      sHash_[atid1] |= STICKY_INTERACTION;
149 >    }
150 >    if (atype1->isStickyPower()) {
151 >      sHash_[atid1] |= STICKY_INTERACTION;
152 >    }
153 >    if (atype1->isEAM()) {
154 >      sHash_[atid1] |= EAM_INTERACTION;
155 >    }
156 >    if (atype1->isSC()) {
157 >      sHash_[atid1] |= SC_INTERACTION;
158 >    }
159 >    if (atype1->isGayBerne()) {
160 >      sHash_[atid1] |= GB_INTERACTION;
161 >    }
162 >  
163      // Now, iterate over all known types and add to the interaction map:
164      
165      map<int, AtomType*>::iterator it1, it2;
166      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
167        atype1 = (*it1).second;
168 +      atid1 = atype1->getIdent();
169  
170        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
171          atype2 = (*it2).second;
172 +        atid2 = atype2->getIdent();
173 +                              
174 +        iHash_[atid1][atid2] = 0;
175          
135 –        bool vdwExplicit = false;
136 –        bool metExplicit = false;
137 –        bool hbExplicit = false;
138 –                      
139 –        key = make_pair(atype1, atype2);
140 –        
176          if (atype1->isLennardJones() && atype2->isLennardJones()) {
177 <          interactions_[key].insert(lj_);
177 >          interactions_[atid1][atid2].insert(lj_);
178 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
179          }
180          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
181 <          interactions_[key].insert(electrostatic_);
181 >          interactions_[atid1][atid2].insert(electrostatic_);
182 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
183          }
184          if (atype1->isSticky() && atype2->isSticky() ) {
185 <          interactions_[key].insert(sticky_);
185 >          interactions_[atid1][atid2].insert(sticky_);
186 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
187          }
188          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
189 <          interactions_[key].insert(sticky_);
189 >          interactions_[atid1][atid2].insert(sticky_);
190 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
191          }
192          if (atype1->isEAM() && atype2->isEAM() ) {
193 <          interactions_[key].insert(eam_);
193 >          interactions_[atid1][atid2].insert(eam_);
194 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
195          }
196          if (atype1->isSC() && atype2->isSC() ) {
197 <          interactions_[key].insert(sc_);
197 >          interactions_[atid1][atid2].insert(sc_);
198 >          iHash_[atid1][atid2] |= SC_INTERACTION;
199          }
200          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
201 <          interactions_[key].insert(gb_);
201 >          interactions_[atid1][atid2].insert(gb_);
202 >          iHash_[atid1][atid2] |= GB_INTERACTION;
203          }
204          if ((atype1->isGayBerne() && atype2->isLennardJones())
205              || (atype1->isLennardJones() && atype2->isGayBerne())) {
206 <          interactions_[key].insert(gb_);
206 >          interactions_[atid1][atid2].insert(gb_);
207 >          iHash_[atid1][atid2] |= GB_INTERACTION;
208          }
209          
210          // look for an explicitly-set non-bonded interaction type using the
211          // two atom types.
212          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
213 +        
214 +        if (nbiType != NULL) {
215  
216 <        if (nbiType->isLennardJones()) {
217 <          // We found an explicit Lennard-Jones interaction.  
218 <          // override all other vdw entries for this pair of atom types:
219 <          set<NonBondedInteraction*>::iterator it;
220 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
221 <            InteractionFamily ifam = (*it)->getFamily();
222 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
223 <          }
224 <          interactions_[key].insert(lj_);
225 <          vdwExplicit = true;
226 <        }
227 <
228 <        if (nbiType->isMorse()) {
229 <          if (vdwExplicit) {
230 <            sprintf( painCave.errMsg,
231 <                     "InteractionManager::initialize found more than one explicit\n"
232 <                     "\tvan der Waals interaction for atom types %s - %s\n",
233 <                     atype1->getName().c_str(), atype2->getName().c_str());
234 <            painCave.severity = OPENMD_ERROR;
190 <            painCave.isFatal = 1;
191 <            simError();
216 >          bool vdwExplicit = false;
217 >          bool metExplicit = false;
218 >          // bool hbExplicit = false;
219 >
220 >          if (nbiType->isLennardJones()) {
221 >            // We found an explicit Lennard-Jones interaction.  
222 >            // override all other vdw entries for this pair of atom types:
223 >            set<NonBondedInteraction*>::iterator it;
224 >            for (it = interactions_[atid1][atid2].begin();
225 >                 it != interactions_[atid1][atid2].end(); ++it) {
226 >              InteractionFamily ifam = (*it)->getFamily();
227 >              if (ifam == VANDERWAALS_FAMILY) {
228 >                interactions_[atid1][atid2].erase(*it);
229 >                iHash_[atid1][atid2] ^= (*it)->getHash();
230 >              }
231 >            }
232 >            interactions_[atid1][atid2].insert(lj_);
233 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
234 >            vdwExplicit = true;
235            }
236 <          // We found an explicit Morse interaction.  
237 <          // override all other vdw entries for this pair of atom types:
238 <          set<NonBondedInteraction*>::iterator it;
239 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
240 <            InteractionFamily ifam = (*it)->getFamily();
241 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
236 >          
237 >          if (nbiType->isMorse()) {
238 >            if (vdwExplicit) {
239 >              sprintf( painCave.errMsg,
240 >                       "InteractionManager::initialize found more than one "
241 >                       "explicit \n"
242 >                       "\tvan der Waals interaction for atom types %s - %s\n",
243 >                       atype1->getName().c_str(), atype2->getName().c_str());
244 >              painCave.severity = OPENMD_ERROR;
245 >              painCave.isFatal = 1;
246 >              simError();
247 >            }
248 >            // We found an explicit Morse interaction.  
249 >            // override all other vdw entries for this pair of atom types:
250 >            set<NonBondedInteraction*>::iterator it;
251 >            for (it = interactions_[atid1][atid2].begin();
252 >                 it != interactions_[atid1][atid2].end(); ++it) {
253 >              InteractionFamily ifam = (*it)->getFamily();
254 >              if (ifam == VANDERWAALS_FAMILY) {
255 >                interactions_[atid1][atid2].erase(*it);
256 >                iHash_[atid1][atid2] ^= (*it)->getHash();
257 >              }
258 >            }
259 >            interactions_[atid1][atid2].insert(morse_);
260 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
261 >            vdwExplicit = true;
262            }
200 –          interactions_[key].insert(morse_);
201 –          vdwExplicit = true;
202 –        }
263  
264 <        if (nbiType->isEAM()) {
265 <          // We found an explicit EAM interaction.  
266 <          // override all other metallic entries for this pair of atom types:
267 <          set<NonBondedInteraction*>::iterator it;
268 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
269 <            InteractionFamily ifam = (*it)->getFamily();
270 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
264 >          if (nbiType->isRepulsivePower()) {
265 >            if (vdwExplicit) {
266 >              sprintf( painCave.errMsg,
267 >                       "InteractionManager::initialize found more than one "
268 >                       "explicit \n"
269 >                       "\tvan der Waals interaction for atom types %s - %s\n",
270 >                       atype1->getName().c_str(), atype2->getName().c_str());
271 >              painCave.severity = OPENMD_ERROR;
272 >              painCave.isFatal = 1;
273 >              simError();
274 >            }
275 >            // We found an explicit RepulsivePower interaction.  
276 >            // override all other vdw entries for this pair of atom types:
277 >            set<NonBondedInteraction*>::iterator it;
278 >            for (it = interactions_[atid1][atid2].begin();
279 >                 it != interactions_[atid1][atid2].end(); ++it) {
280 >              InteractionFamily ifam = (*it)->getFamily();
281 >              if (ifam == VANDERWAALS_FAMILY) {
282 >                interactions_[atid1][atid2].erase(*it);
283 >                iHash_[atid1][atid2] ^= (*it)->getHash();
284 >              }
285 >            }
286 >            interactions_[atid1][atid2].insert(repulsivePower_);
287 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
288 >            vdwExplicit = true;
289            }
290 <          interactions_[key].insert(eam_);
291 <          metExplicit = true;
292 <        }
293 <
294 <        if (nbiType->isSC()) {
295 <          if (metExplicit) {
296 <            sprintf( painCave.errMsg,
297 <                     "InteractionManager::initialize found more than one explicit\n"
298 <                     "\tmetallic interaction for atom types %s - %s\n",
299 <                     atype1->getName().c_str(), atype2->getName().c_str());
300 <            painCave.severity = OPENMD_ERROR;
301 <            painCave.isFatal = 1;
302 <            simError();
290 >          
291 >          
292 >          if (nbiType->isEAM()) {
293 >            // We found an explicit EAM interaction.  
294 >            // override all other metallic entries for this pair of atom types:
295 >            set<NonBondedInteraction*>::iterator it;
296 >            for (it = interactions_[atid1][atid2].begin();
297 >                 it != interactions_[atid1][atid2].end(); ++it) {
298 >              InteractionFamily ifam = (*it)->getFamily();
299 >              if (ifam == METALLIC_FAMILY) {
300 >                interactions_[atid1][atid2].erase(*it);
301 >                iHash_[atid1][atid2] ^= (*it)->getHash();
302 >              }
303 >            }
304 >            interactions_[atid1][atid2].insert(eam_);
305 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
306 >            metExplicit = true;
307            }
308 <          // We found an explicit Sutton-Chen interaction.  
309 <          // override all other metallic entries for this pair of atom types:
310 <          set<NonBondedInteraction*>::iterator it;
311 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
312 <            InteractionFamily ifam = (*it)->getFamily();
313 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
308 >          
309 >          if (nbiType->isSC()) {
310 >            if (metExplicit) {
311 >              sprintf( painCave.errMsg,
312 >                       "InteractionManager::initialize found more than one "
313 >                       "explicit\n"
314 >                       "\tmetallic interaction for atom types %s - %s\n",
315 >                       atype1->getName().c_str(), atype2->getName().c_str());
316 >              painCave.severity = OPENMD_ERROR;
317 >              painCave.isFatal = 1;
318 >              simError();
319 >            }
320 >            // We found an explicit Sutton-Chen interaction.  
321 >            // override all other metallic entries for this pair of atom types:
322 >            set<NonBondedInteraction*>::iterator it;
323 >            for (it = interactions_[atid1][atid2].begin();
324 >                 it != interactions_[atid1][atid2].end(); ++it) {
325 >              InteractionFamily ifam = (*it)->getFamily();
326 >              if (ifam == METALLIC_FAMILY) {
327 >                interactions_[atid1][atid2].erase(*it);
328 >                iHash_[atid1][atid2] ^= (*it)->getHash();
329 >              }
330 >            }
331 >            interactions_[atid1][atid2].insert(sc_);
332 >            iHash_[atid1][atid2] |= SC_INTERACTION;
333 >            metExplicit = true;
334            }
335 <          interactions_[key].insert(sc_);
336 <          metExplicit = true;
335 >          
336 >          if (nbiType->isMAW()) {
337 >            if (vdwExplicit) {
338 >              sprintf( painCave.errMsg,
339 >                       "InteractionManager::initialize found more than one "
340 >                       "explicit\n"
341 >                       "\tvan der Waals interaction for atom types %s - %s\n",
342 >                       atype1->getName().c_str(), atype2->getName().c_str());
343 >              painCave.severity = OPENMD_ERROR;
344 >              painCave.isFatal = 1;
345 >              simError();
346 >            }
347 >            // We found an explicit MAW interaction.  
348 >            // override all other vdw entries for this pair of atom types:
349 >            set<NonBondedInteraction*>::iterator it;
350 >            for (it = interactions_[atid1][atid2].begin();
351 >                 it != interactions_[atid1][atid2].end(); ++it) {
352 >              InteractionFamily ifam = (*it)->getFamily();
353 >              if (ifam == VANDERWAALS_FAMILY) {
354 >                interactions_[atid1][atid2].erase(*it);
355 >                iHash_[atid1][atid2] ^= (*it)->getHash();
356 >              }
357 >            }
358 >            interactions_[atid1][atid2].insert(maw_);
359 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
360 >            vdwExplicit = true;
361 >          }        
362          }
236 –
237 –        if (nbiType->isMAW()) {
238 –          if (vdwExplicit) {
239 –            sprintf( painCave.errMsg,
240 –                     "InteractionManager::initialize found more than one explicit\n"
241 –                     "\tvan der Waals interaction for atom types %s - %s\n",
242 –                     atype1->getName().c_str(), atype2->getName().c_str());
243 –            painCave.severity = OPENMD_ERROR;
244 –            painCave.isFatal = 1;
245 –            simError();
246 –          }
247 –          // We found an explicit MAW interaction.  
248 –          // override all other vdw entries for this pair of atom types:
249 –          set<NonBondedInteraction*>::iterator it;
250 –          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
251 –            InteractionFamily ifam = (*it)->getFamily();
252 –            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
253 –          }
254 –          interactions_[key].insert(maw_);
255 –          vdwExplicit = true;
256 –        }        
363        }
364      }
365      
366 <    // make sure every pair of atom types has a non-bonded interaction:
367 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
368 <         atype1 = atomTypes->nextType(i1)) {
369 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
370 <           atype2 = atomTypes->nextType(i2)) {
371 <        key = make_pair(atype1, atype2);
366 >    
367 >    // Make sure every pair of atom types in this simulation has a
368 >    // non-bonded interaction.  If not, just inform the user.
369 >
370 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
371 >    set<AtomType*>::iterator it, jt;
372 >
373 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
374 >      atype1 = (*it);
375 >      atid1 = atype1->getIdent();
376 >      for (jt = it; jt != simTypes.end(); ++jt) {
377 >        atype2 = (*jt);
378 >        atid1 = atype1->getIdent();
379          
380 <        if (interactions_[key].size() == 0) {
380 >        if (interactions_[atid1][atid2].size() == 0) {
381            sprintf( painCave.errMsg,
382 <                   "InteractionManager unable to find an appropriate non-bonded\n"
383 <                   "\tinteraction for atom types %s - %s\n",
382 >                   "InteractionManager could not find a matching non-bonded\n"
383 >                   "\tinteraction for atom types %s - %s\n"
384 >                   "\tProceeding without this interaction.\n",
385                     atype1->getName().c_str(), atype2->getName().c_str());
386            painCave.severity = OPENMD_INFO;
387 <          painCave.isFatal = 1;
387 >          painCave.isFatal = 0;
388            simError();
389          }
390        }
391      }
392 <  }
393 <  
394 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
392 >
393 >    initialized_ = true;
394 >  }
395 >
396 >  void InteractionManager::setCutoffRadius(RealType rcut) {
397      
398 +    electrostatic_->setCutoffRadius(rcut);
399 +    eam_->setCutoffRadius(rcut);
400 +  }
401 +
402 +  void InteractionManager::doPrePair(InteractionData &idat){
403 +    
404      if (!initialized_) initialize();
405 <          
406 <    DensityData ddat;
405 >        
406 >    // excluded interaction, so just return
407 >    if (idat.excluded) return;
408  
409 <    ddat.atype1 = typeMap_[*atid1];
287 <    ddat.atype2 = typeMap_[*atid2];
288 <    ddat.rij = *rij;
289 <    ddat.rho_i_at_j = *rho_i_at_j;
290 <    ddat.rho_j_at_i = *rho_j_at_i;
409 >    int& iHash = iHash_[idat.atid1][idat.atid2];
410  
411 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
412 <    set<NonBondedInteraction*>::iterator it;
411 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
412 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
413  
414 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
415 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
416 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
417 <      }
418 <    }
414 >    // set<NonBondedInteraction*>::iterator it;
415 >
416 >    // for (it = interactions_[ idat.atypes ].begin();
417 >    //      it != interactions_[ idat.atypes ].end(); ++it){
418 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
419 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
420 >    //   }
421 >    // }
422      
423      return;    
424    }
425    
426 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
426 >  void InteractionManager::doPreForce(SelfData &sdat){
427  
428      if (!initialized_) initialize();
429 <          
430 <    FunctionalData fdat;
429 >    
430 >    int& sHash = sHash_[sdat.atid];
431  
432 <    fdat.atype = typeMap_[*atid];
433 <    fdat.rho = *rho;
312 <    fdat.frho = *frho;
313 <    fdat.dfrhodrho = *dfrhodrho;
432 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
433 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
434  
435 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
316 <    set<NonBondedInteraction*>::iterator it;
435 >    // set<NonBondedInteraction*>::iterator it;
436      
437 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
438 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
439 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
440 <      }
441 <    }
437 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
438 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
439 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
440 >    //   }
441 >    // }
442      
443      return;    
444    }
445  
446 <  void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, int *topoDist, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){
446 >  void InteractionManager::doPair(InteractionData &idat){
447      
448      if (!initialized_) initialize();
330 –    
331 –    InteractionData idat;
332 –    
333 –    idat.atype1 = typeMap_[*atid1];
334 –    idat.atype2 = typeMap_[*atid2];
335 –    idat.d = Vector3d(d);
336 –    idat.rij = *r;
337 –    idat.r2 = *r2;
338 –    idat.rcut = *rcut;
339 –    idat.sw = *sw;
340 –    idat.vdwMult = vdwScale_[*topoDist];
341 –    idat.electroMult = electrostaticScale_[*topoDist];
342 –    idat.pot = *pot;
343 –    idat.vpair = *vpair;
344 –    idat.f1 = Vector3d(f1);
345 –    idat.eFrame1 = Mat3x3d(eFrame1);
346 –    idat.eFrame2 = Mat3x3d(eFrame2);
347 –    idat.A1 = RotMat3x3d(A1);
348 –    idat.A2 = RotMat3x3d(A2);
349 –    idat.t1 = Vector3d(t1);
350 –    idat.t2 = Vector3d(t2);
351 –    idat.rho1 = *rho1;
352 –    idat.rho2 = *rho2;
353 –    idat.dfrho1 = *dfrho1;
354 –    idat.dfrho2 = *dfrho2;
355 –    idat.fshift1 = *fshift1;
356 –    idat.fshift2 = *fshift2;
449  
450 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
359 <    set<NonBondedInteraction*>::iterator it;
450 >    int& iHash = iHash_[idat.atid1][idat.atid2];
451  
452 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
453 <      (*it)->calcForce(idat);
454 <    
455 <    f1[0] = idat.f1.x();
365 <    f1[1] = idat.f1.y();
366 <    f1[2] = idat.f1.z();
367 <    
368 <    t1[0] = idat.t1.x();
369 <    t1[1] = idat.t1.y();
370 <    t1[2] = idat.t1.z();
371 <    
372 <    t2[0] = idat.t2.x();
373 <    t2[1] = idat.t2.y();
374 <    t2[2] = idat.t2.z();
452 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
453 >      
454 >    // electrostatics still has to worry about indirect
455 >    // contributions from excluded pairs of atoms, but nothing else does:
456  
457 <    return;    
377 <  }
457 >    if (idat.excluded) return;
458  
459 <  void InteractionManager::doSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){
459 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
460 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
461 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
462 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
463 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
464 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
465 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
466 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
467  
468 <    if (!initialized_) initialize();
382 <    
383 <    SkipCorrectionData skdat;
384 <    
385 <    skdat.atype1 = typeMap_[*atid1];
386 <    skdat.atype2 = typeMap_[*atid2];
387 <    skdat.d = Vector3d(d);
388 <    skdat.rij = *r;
389 <    skdat.skippedCharge1 = *skippedCharge1;
390 <    skdat.skippedCharge2 = *skippedCharge2;
391 <    skdat.sw = *sw;
392 <    skdat.electroMult = *electroMult;
393 <    skdat.pot = *pot;
394 <    skdat.vpair = *vpair;
395 <    skdat.f1 = Vector3d(f1);
396 <    skdat.eFrame1 = Mat3x3d(eFrame1);
397 <    skdat.eFrame2 = Mat3x3d(eFrame2);
398 <    skdat.t1 = Vector3d(t1);
399 <    skdat.t2 = Vector3d(t2);
468 >    // set<NonBondedInteraction*>::iterator it;
469  
470 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
471 <    set<NonBondedInteraction*>::iterator it;
470 >    // for (it = interactions_[ idat.atypes ].begin();
471 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
472  
473 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
474 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
406 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
407 <      }
408 <    }
409 <    
410 <    f1[0] = skdat.f1.x();
411 <    f1[1] = skdat.f1.y();
412 <    f1[2] = skdat.f1.z();
413 <    
414 <    t1[0] = skdat.t1.x();
415 <    t1[1] = skdat.t1.y();
416 <    t1[2] = skdat.t1.z();
417 <    
418 <    t2[0] = skdat.t2.x();
419 <    t2[1] = skdat.t2.y();
420 <    t2[2] = skdat.t2.z();
473 >    //   // electrostatics still has to worry about indirect
474 >    //   // contributions from excluded pairs of atoms:
475  
476 +    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
477 +    //     (*it)->calcForce(idat);
478 +    //   }
479 +    // }
480 +    
481      return;    
482    }
483  
484 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
484 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
485  
486      if (!initialized_) initialize();
487      
488 <    SelfCorrectionData scdat;
430 <    
431 <    scdat.atype = typeMap_[*atid];
432 <    scdat.eFrame = Mat3x3d(eFrame);
433 <    scdat.skippedCharge = *skippedCharge;
434 <    scdat.pot = *pot;
435 <    scdat.t = Vector3d(t);
488 >    int& sHash = sHash_[sdat.atid];
489  
490 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
438 <    set<NonBondedInteraction*>::iterator it;
490 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
491  
492 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
441 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
442 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
443 <      }
444 <    }
445 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
492 >    // set<NonBondedInteraction*>::iterator it;
493  
494 +    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
495 +    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
496 +    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
497 +    //   }
498 +    // }
499 +      
500      return;    
501    }
502  
503 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
504 +    if (!initialized_) initialize();
505 +    electrostatic_->ReciprocalSpaceSum(pot);
506 +  }
507  
508    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
509      if (!initialized_) initialize();
510 <    
510 >
511      AtomType* atype = typeMap_[*atid];
512  
459 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
513      set<NonBondedInteraction*>::iterator it;
514      RealType cutoff = 0.0;
515      
516 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
517 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
516 >    for (it = interactions_[*atid][*atid].begin();
517 >         it != interactions_[*atid][*atid].end();
518 >         ++it)
519 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
520      return cutoff;    
521    }
522  
523    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
524      if (!initialized_) initialize();
525      
526 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
526 >    int atid = atype->getIdent();
527 >
528      set<NonBondedInteraction*>::iterator it;
529      RealType cutoff = 0.0;
530      
531 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
532 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
531 >    for (it = interactions_[atid][atid].begin();
532 >         it != interactions_[atid][atid].end(); ++it)
533 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
534      return cutoff;    
535    }
479 –
480 –
481 –  void InteractionManager::setSwitch(RealType *rIn, RealType *rOut) {
482 –    switcher_->setSwitch(*rIn, *rOut);    
483 –  }
484 –
485 –  void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
486 –                                     int *in_switching_region) {
487 –    bool isr = switcher_->getSwitch(*r2, *sw, *dswdr, *r);    
488 –    *in_switching_region = (int)isr;
489 –  }
490 –
536   } //end namespace OpenMD
492 –
493 – extern "C" {
494 –  
495 – #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
496 – #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
497 – #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
498 – #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
499 – #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
500 – #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
501 – #define fortranSetSwitch FC_FUNC(set_switch, SET_SWITCH)
502 – #define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH)
503 –
504 –  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
505 –                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
506 –            
507 –    return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij,
508 –                                                             rho_i_at_j,  
509 –                                                             rho_j_at_i);
510 –  }
511 –  void fortranDoPreForce(int *atid, RealType *rho, RealType *frho,
512 –                         RealType *dfrhodrho) {  
513 –    
514 –    return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho,
515 –                                                              dfrhodrho);    
516 –  }
517 –  
518 –  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r,
519 –                     RealType *r2, RealType *rcut, RealType *sw, int *topoDist,
520 –                     RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1,
521 –                     RealType *eFrame2, RealType *A1, RealType *A2,
522 –                     RealType *t1, RealType *t2, RealType *rho1, RealType *rho2,
523 –                     RealType *dfrho1, RealType *dfrho2, RealType *fshift1,
524 –                     RealType *fshift2){
525 –    
526 –    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r,
527 –                                                          r2, rcut, sw, topoDist,
528 –                                                          pot, vpair, f1,
529 –                                                          eFrame1, eFrame2,
530 –                                                          A1, A2, t1, t2, rho1,
531 –                                                          rho2, dfrho1, dfrho2,
532 –                                                          fshift1, fshift2);
533 –  }
534 –  
535 –  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d,
536 –                               RealType *r, RealType *skippedCharge1,
537 –                               RealType *skippedCharge2, RealType *sw,
538 –                               RealType *electroMult, RealType *pot,
539 –                               RealType *vpair, RealType *f1,
540 –                               RealType *eFrame1, RealType *eFrame2,
541 –                               RealType *t1, RealType *t2){
542 –    
543 –    return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1,
544 –                                                                    atid2, d,
545 –                                                                    r,
546 –                                                                    skippedCharge1,
547 –                                                                    skippedCharge2,
548 –                                                                    sw, electroMult, pot,
549 –                                                                    vpair, f1, eFrame1,
550 –                                                                    eFrame2, t1, t2);
551 –  }
552 –  
553 –  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
554 –                               RealType *pot, RealType *t) {
555 –    
556 –    return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid,
557 –                                                                    eFrame,
558 –                                                                    skippedCharge,
559 –                                                                    pot, t);
560 –  }
561 –  RealType fortranGetCutoff(int *atid) {    
562 –    return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid);
563 –  }
564 –
565 –  void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
566 –                        int *in_switching_region) {
567 –    
568 –    return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r,
569 –                                                             in_switching_region);
570 –  }
571 –
572 –  void fortranSetSwitch(RealType *rIn, RealType *rOut) {    
573 –    return OpenMD::InteractionManager::Instance()->setSwitch(rIn, rOut);
574 –  }
575 –  
576 – }

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