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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 2005 by gezelter, Wed Jun 11 18:37:56 2014 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;
101 <    
102 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
103 <         atype1 = atomTypes->nextType(i1)) {
104 <      
105 <      // add it to the map:
106 <      AtomTypeProperties atp = atype1->getATP();    
107 <      
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 >      atype1 = *at;
121 >      atid1 = atype1->getIdent();
122 >      iHash_[atid1].resize(nTypes);
123 >      interactions_[atid1].resize(nTypes);
124 >
125 >      // add it to the map:      
126        pair<map<int,AtomType*>::iterator,bool> ret;    
127 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
127 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
128        if (ret.second == false) {
129          sprintf( painCave.errMsg,
130                   "InteractionManager already had a previous entry with ident %d\n",
131 <                 atp.ident);
131 >                 atype1->getIdent());
132          painCave.severity = OPENMD_INFO;
133          painCave.isFatal = 0;
134          simError();                
135        }
136 +          
137 +      if (atype1->isLennardJones()) {
138 +        sHash_[atid1] |= LJ_INTERACTION;
139 +      }
140 +      if (atype1->isElectrostatic()) {
141 +        sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
142 +      }
143 +      if (atype1->isSticky()) {
144 +        sHash_[atid1] |= STICKY_INTERACTION;
145 +      }
146 +      if (atype1->isStickyPower()) {
147 +        sHash_[atid1] |= STICKY_INTERACTION;
148 +      }
149 +      if (atype1->isEAM()) {      
150 +        sHash_[atid1] |= EAM_INTERACTION;
151 +      }
152 +      if (atype1->isSC()) {
153 +        sHash_[atid1] |= SC_INTERACTION;
154 +      }
155 +      if (atype1->isGayBerne()) {
156 +        sHash_[atid1] |= GB_INTERACTION;
157 +      }
158      }
125 –    
159      // Now, iterate over all known types and add to the interaction map:
160      
161      map<int, AtomType*>::iterator it1, it2;
162      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
163        atype1 = (*it1).second;
164 +      atid1 = atype1->getIdent();
165  
166        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
167          atype2 = (*it2).second;
168 +        atid2 = atype2->getIdent();
169 +                              
170 +        iHash_[atid1][atid2] = 0;
171          
135 –        bool vdwExplicit = false;
136 –        bool metExplicit = false;
137 –        bool hbExplicit = false;
138 –                      
139 –        key = make_pair(atype1, atype2);
140 –        
172          if (atype1->isLennardJones() && atype2->isLennardJones()) {
173 <          interactions_[key].insert(lj_);
173 >          interactions_[atid1][atid2].insert(lj_);
174 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
175          }
176          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
177 <          interactions_[key].insert(electrostatic_);
177 >          interactions_[atid1][atid2].insert(electrostatic_);
178 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
179          }
180          if (atype1->isSticky() && atype2->isSticky() ) {
181 <          interactions_[key].insert(sticky_);
181 >          interactions_[atid1][atid2].insert(sticky_);
182 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
183          }
184          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
185 <          interactions_[key].insert(sticky_);
185 >          interactions_[atid1][atid2].insert(sticky_);
186 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
187          }
188          if (atype1->isEAM() && atype2->isEAM() ) {
189 <          interactions_[key].insert(eam_);
189 >          interactions_[atid1][atid2].insert(eam_);
190 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
191          }
192          if (atype1->isSC() && atype2->isSC() ) {
193 <          interactions_[key].insert(sc_);
193 >          interactions_[atid1][atid2].insert(sc_);
194 >          iHash_[atid1][atid2] |= SC_INTERACTION;
195          }
196          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
197 <          interactions_[key].insert(gb_);
197 >          interactions_[atid1][atid2].insert(gb_);
198 >          iHash_[atid1][atid2] |= GB_INTERACTION;
199          }
200          if ((atype1->isGayBerne() && atype2->isLennardJones())
201              || (atype1->isLennardJones() && atype2->isGayBerne())) {
202 <          interactions_[key].insert(gb_);
202 >          interactions_[atid1][atid2].insert(gb_);
203 >          iHash_[atid1][atid2] |= GB_INTERACTION;
204          }
205          
206          // look for an explicitly-set non-bonded interaction type using the
207          // two atom types.
208          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
209 +        
210 +        if (nbiType != NULL) {
211  
212 <        if (nbiType->isLennardJones()) {
213 <          // We found an explicit Lennard-Jones interaction.  
214 <          // override all other vdw entries for this pair of atom types:
215 <          set<NonBondedInteraction*>::iterator it;
216 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
217 <            InteractionFamily ifam = (*it)->getFamily();
218 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
219 <          }
220 <          interactions_[key].insert(lj_);
221 <          vdwExplicit = true;
222 <        }
223 <
224 <        if (nbiType->isMorse()) {
225 <          if (vdwExplicit) {
226 <            sprintf( painCave.errMsg,
227 <                     "InteractionManager::initialize found more than one explicit\n"
228 <                     "\tvan der Waals interaction for atom types %s - %s\n",
229 <                     atype1->getName().c_str(), atype2->getName().c_str());
230 <            painCave.severity = OPENMD_ERROR;
190 <            painCave.isFatal = 1;
191 <            simError();
212 >          bool vdwExplicit = false;
213 >          bool metExplicit = false;
214 >          // bool hbExplicit = false;
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_[atid1][atid2].begin();
221 >                 it != interactions_[atid1][atid2].end(); ++it) {
222 >              InteractionFamily ifam = (*it)->getFamily();
223 >              if (ifam == VANDERWAALS_FAMILY) {
224 >                interactions_[atid1][atid2].erase(*it);
225 >                iHash_[atid1][atid2] ^= (*it)->getHash();
226 >              }
227 >            }
228 >            interactions_[atid1][atid2].insert(lj_);
229 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
230 >            vdwExplicit = true;
231            }
232 <          // We found an explicit Morse interaction.  
233 <          // override all other vdw entries for this pair of atom types:
234 <          set<NonBondedInteraction*>::iterator it;
235 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
236 <            InteractionFamily ifam = (*it)->getFamily();
237 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
232 >          
233 >          if (nbiType->isMorse()) {
234 >            if (vdwExplicit) {
235 >              sprintf( painCave.errMsg,
236 >                       "InteractionManager::initialize found more than one "
237 >                       "explicit \n"
238 >                       "\tvan der Waals interaction for atom types %s - %s\n",
239 >                       atype1->getName().c_str(), atype2->getName().c_str());
240 >              painCave.severity = OPENMD_ERROR;
241 >              painCave.isFatal = 1;
242 >              simError();
243 >            }
244 >            // We found an explicit Morse interaction.  
245 >            // override all other vdw entries for this pair of atom types:
246 >            set<NonBondedInteraction*>::iterator it;
247 >            for (it = interactions_[atid1][atid2].begin();
248 >                 it != interactions_[atid1][atid2].end(); ++it) {
249 >              InteractionFamily ifam = (*it)->getFamily();
250 >              if (ifam == VANDERWAALS_FAMILY) {
251 >                interactions_[atid1][atid2].erase(*it);
252 >                iHash_[atid1][atid2] ^= (*it)->getHash();
253 >              }
254 >            }
255 >            interactions_[atid1][atid2].insert(morse_);
256 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
257 >            vdwExplicit = true;
258            }
200 –          interactions_[key].insert(morse_);
201 –          vdwExplicit = true;
202 –        }
259  
260 <        if (nbiType->isEAM()) {
261 <          // We found an explicit EAM interaction.  
262 <          // override all other metallic entries for this pair of atom types:
263 <          set<NonBondedInteraction*>::iterator it;
264 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
265 <            InteractionFamily ifam = (*it)->getFamily();
266 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
260 >          if (nbiType->isRepulsivePower()) {
261 >            if (vdwExplicit) {
262 >              sprintf( painCave.errMsg,
263 >                       "InteractionManager::initialize found more than one "
264 >                       "explicit \n"
265 >                       "\tvan der Waals interaction for atom types %s - %s\n",
266 >                       atype1->getName().c_str(), atype2->getName().c_str());
267 >              painCave.severity = OPENMD_ERROR;
268 >              painCave.isFatal = 1;
269 >              simError();
270 >            }
271 >            // We found an explicit RepulsivePower interaction.  
272 >            // override all other vdw entries for this pair of atom types:
273 >            set<NonBondedInteraction*>::iterator it;
274 >            for (it = interactions_[atid1][atid2].begin();
275 >                 it != interactions_[atid1][atid2].end(); ++it) {
276 >              InteractionFamily ifam = (*it)->getFamily();
277 >              if (ifam == VANDERWAALS_FAMILY) {
278 >                interactions_[atid1][atid2].erase(*it);
279 >                iHash_[atid1][atid2] ^= (*it)->getHash();
280 >              }
281 >            }
282 >            interactions_[atid1][atid2].insert(repulsivePower_);
283 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
284 >            vdwExplicit = true;
285            }
286 <          interactions_[key].insert(eam_);
287 <          metExplicit = true;
288 <        }
289 <
290 <        if (nbiType->isSC()) {
291 <          if (metExplicit) {
292 <            sprintf( painCave.errMsg,
293 <                     "InteractionManager::initialize found more than one explicit\n"
294 <                     "\tmetallic interaction for atom types %s - %s\n",
295 <                     atype1->getName().c_str(), atype2->getName().c_str());
296 <            painCave.severity = OPENMD_ERROR;
297 <            painCave.isFatal = 1;
298 <            simError();
286 >          
287 >          
288 >          if (nbiType->isEAM()) {
289 >            // We found an explicit EAM interaction.  
290 >            // override all other metallic entries for this pair of atom types:
291 >            set<NonBondedInteraction*>::iterator it;
292 >            for (it = interactions_[atid1][atid2].begin();
293 >                 it != interactions_[atid1][atid2].end(); ++it) {
294 >              InteractionFamily ifam = (*it)->getFamily();
295 >              if (ifam == METALLIC_FAMILY) {
296 >                interactions_[atid1][atid2].erase(*it);
297 >                iHash_[atid1][atid2] ^= (*it)->getHash();
298 >              }
299 >            }
300 >            interactions_[atid1][atid2].insert(eam_);
301 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
302 >            metExplicit = true;
303            }
304 <          // We found an explicit Sutton-Chen interaction.  
305 <          // override all other metallic entries for this pair of atom types:
306 <          set<NonBondedInteraction*>::iterator it;
307 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
308 <            InteractionFamily ifam = (*it)->getFamily();
309 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
304 >          
305 >          if (nbiType->isSC()) {
306 >            if (metExplicit) {
307 >              sprintf( painCave.errMsg,
308 >                       "InteractionManager::initialize found more than one "
309 >                       "explicit\n"
310 >                       "\tmetallic interaction for atom types %s - %s\n",
311 >                       atype1->getName().c_str(), atype2->getName().c_str());
312 >              painCave.severity = OPENMD_ERROR;
313 >              painCave.isFatal = 1;
314 >              simError();
315 >            }
316 >            // We found an explicit Sutton-Chen interaction.  
317 >            // override all other metallic entries for this pair of atom types:
318 >            set<NonBondedInteraction*>::iterator it;
319 >            for (it = interactions_[atid1][atid2].begin();
320 >                 it != interactions_[atid1][atid2].end(); ++it) {
321 >              InteractionFamily ifam = (*it)->getFamily();
322 >              if (ifam == METALLIC_FAMILY) {
323 >                interactions_[atid1][atid2].erase(*it);
324 >                iHash_[atid1][atid2] ^= (*it)->getHash();
325 >              }
326 >            }
327 >            interactions_[atid1][atid2].insert(sc_);
328 >            iHash_[atid1][atid2] |= SC_INTERACTION;
329 >            metExplicit = true;
330            }
331 <          interactions_[key].insert(sc_);
332 <          metExplicit = true;
331 >          
332 >          if (nbiType->isMAW()) {
333 >            if (vdwExplicit) {
334 >              sprintf( painCave.errMsg,
335 >                       "InteractionManager::initialize found more than one "
336 >                       "explicit\n"
337 >                       "\tvan der Waals interaction for atom types %s - %s\n",
338 >                       atype1->getName().c_str(), atype2->getName().c_str());
339 >              painCave.severity = OPENMD_ERROR;
340 >              painCave.isFatal = 1;
341 >              simError();
342 >            }
343 >            // We found an explicit MAW interaction.  
344 >            // override all other vdw entries for this pair of atom types:
345 >            set<NonBondedInteraction*>::iterator it;
346 >            for (it = interactions_[atid1][atid2].begin();
347 >                 it != interactions_[atid1][atid2].end(); ++it) {
348 >              InteractionFamily ifam = (*it)->getFamily();
349 >              if (ifam == VANDERWAALS_FAMILY) {
350 >                interactions_[atid1][atid2].erase(*it);
351 >                iHash_[atid1][atid2] ^= (*it)->getHash();
352 >              }
353 >            }
354 >            interactions_[atid1][atid2].insert(maw_);
355 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
356 >            vdwExplicit = true;
357 >          }        
358          }
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 –        }        
359        }
360      }
361      
362 <    // make sure every pair of atom types has a non-bonded interaction:
363 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
364 <         atype1 = atomTypes->nextType(i1)) {
365 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
366 <           atype2 = atomTypes->nextType(i2)) {
367 <        key = make_pair(atype1, atype2);
362 >    
363 >    // Make sure every pair of atom types in this simulation has a
364 >    // non-bonded interaction.  If not, just inform the user.
365 >
366 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
367 >    set<AtomType*>::iterator it, jt;
368 >
369 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
370 >      atype1 = (*it);
371 >      atid1 = atype1->getIdent();
372 >      for (jt = it; jt != simTypes.end(); ++jt) {
373 >        atype2 = (*jt);
374 >        atid2 = atype2->getIdent();
375          
376 <        if (interactions_[key].size() == 0) {
376 >        if (interactions_[atid1][atid2].size() == 0) {
377            sprintf( painCave.errMsg,
378 <                   "InteractionManager unable to find an appropriate non-bonded\n"
379 <                   "\tinteraction for atom types %s - %s\n",
378 >                   "InteractionManager could not find a matching non-bonded\n"
379 >                   "\tinteraction for atom types %s - %s\n"
380 >                   "\tProceeding without this interaction.\n",
381                     atype1->getName().c_str(), atype2->getName().c_str());
382            painCave.severity = OPENMD_INFO;
383 <          painCave.isFatal = 1;
383 >          painCave.isFatal = 0;
384            simError();
385          }
386        }
387      }
388 <  }
389 <  
390 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
388 >
389 >    initialized_ = true;
390 >  }
391 >
392 >  void InteractionManager::setCutoffRadius(RealType rcut) {
393      
394 +    electrostatic_->setCutoffRadius(rcut);
395 +    eam_->setCutoffRadius(rcut);
396 +  }
397 +
398 +  void InteractionManager::doPrePair(InteractionData &idat){
399 +    
400      if (!initialized_) initialize();
401 <          
402 <    DensityData ddat;
401 >        
402 >    // excluded interaction, so just return
403 >    if (idat.excluded) return;
404  
405 <    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;
405 >    int& iHash = iHash_[idat.atid1][idat.atid2];
406  
407 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
408 <    set<NonBondedInteraction*>::iterator it;
407 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
408 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
409  
410 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
411 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
412 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
413 <      }
414 <    }
410 >    // set<NonBondedInteraction*>::iterator it;
411 >
412 >    // for (it = interactions_[ idat.atypes ].begin();
413 >    //      it != interactions_[ idat.atypes ].end(); ++it){
414 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
415 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
416 >    //   }
417 >    // }
418      
419      return;    
420    }
421    
422 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
422 >  void InteractionManager::doPreForce(SelfData &sdat){
423  
424      if (!initialized_) initialize();
425 <          
426 <    FunctionalData fdat;
425 >    
426 >    int& sHash = sHash_[sdat.atid];
427  
428 <    fdat.atype = typeMap_[*atid];
429 <    fdat.rho = *rho;
312 <    fdat.frho = *frho;
313 <    fdat.dfrhodrho = *dfrhodrho;
428 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
429 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
430  
431 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
316 <    set<NonBondedInteraction*>::iterator it;
431 >    // set<NonBondedInteraction*>::iterator it;
432      
433 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
434 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
435 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
436 <      }
437 <    }
433 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
434 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
435 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
436 >    //   }
437 >    // }
438      
439      return;    
440    }
441  
442 <  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){
442 >  void InteractionManager::doPair(InteractionData &idat){
443      
444      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;
445  
446 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
359 <    set<NonBondedInteraction*>::iterator it;
446 >    int& iHash = iHash_[idat.atid1][idat.atid2];
447  
448 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
449 <      (*it)->calcForce(idat);
450 <    
451 <    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();
448 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
449 >      
450 >    // electrostatics still has to worry about indirect
451 >    // contributions from excluded pairs of atoms, but nothing else does:
452  
453 <    return;    
377 <  }
453 >    if (idat.excluded) return;
454  
455 <  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){
455 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
456 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
457 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
458 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
459 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
460 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
461 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
462 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
463  
464 <    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);
464 >    // set<NonBondedInteraction*>::iterator it;
465  
466 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
467 <    set<NonBondedInteraction*>::iterator it;
466 >    // for (it = interactions_[ idat.atypes ].begin();
467 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
468  
469 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
470 <      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();
469 >    //   // electrostatics still has to worry about indirect
470 >    //   // contributions from excluded pairs of atoms:
471  
472 +    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 +    //     (*it)->calcForce(idat);
474 +    //   }
475 +    // }
476 +    
477      return;    
478    }
479  
480 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
480 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
481  
482      if (!initialized_) initialize();
483      
484 <    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);
484 >    int& sHash = sHash_[sdat.atid];
485  
486 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
438 <    set<NonBondedInteraction*>::iterator it;
486 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
487  
488 <    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();
488 >    // set<NonBondedInteraction*>::iterator it;
489  
490 +    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
491 +    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
492 +    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
493 +    //   }
494 +    // }
495 +      
496      return;    
497    }
498  
499 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
500 +    if (!initialized_) initialize();
501 +    electrostatic_->ReciprocalSpaceSum(pot);
502 +  }
503  
504    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
505      if (!initialized_) initialize();
506 <    
506 >
507      AtomType* atype = typeMap_[*atid];
508  
459 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
509      set<NonBondedInteraction*>::iterator it;
510      RealType cutoff = 0.0;
511      
512 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
513 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
512 >    for (it = interactions_[*atid][*atid].begin();
513 >         it != interactions_[*atid][*atid].end();
514 >         ++it)
515 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
516      return cutoff;    
517    }
518  
519    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
520      if (!initialized_) initialize();
521      
522 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
522 >    int atid = atype->getIdent();
523 >
524      set<NonBondedInteraction*>::iterator it;
525      RealType cutoff = 0.0;
526      
527 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
528 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
527 >    for (it = interactions_[atid][atid].begin();
528 >         it != interactions_[atid][atid].end(); ++it)
529 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
530      return cutoff;    
531    }
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 –
532   } //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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