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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 1925 by gezelter, Wed Aug 7 15:24:16 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 +    iHash_.resize(nTypes);
94 +    interactions_.resize(nTypes);
95      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
96      AtomType* atype1;
97      AtomType* atype2;
98 <    pair<AtomType*, AtomType*> key;
99 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
98 >    int atid1, atid2;
99 >
100 >    // We only need to worry about the types that are actually in the simulation:
101 >
102 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
103 >
104 >    lj_->setSimulatedAtomTypes(atypes);
105 >    gb_->setSimulatedAtomTypes(atypes);
106 >    sticky_->setSimulatedAtomTypes(atypes);
107 >    eam_->setSimulatedAtomTypes(atypes);
108 >    sc_->setSimulatedAtomTypes(atypes);
109 >    morse_->setSimulatedAtomTypes(atypes);
110 >    electrostatic_->setSimInfo(info_);
111 >    electrostatic_->setSimulatedAtomTypes(atypes);
112 >    maw_->setSimulatedAtomTypes(atypes);
113 >    repulsivePower_->setSimulatedAtomTypes(atypes);
114 >
115 >    set<AtomType*>::iterator at;
116 >
117 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
118      
119 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 <         atype1 = atomTypes->nextType(i1)) {
119 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 >      //   atype1 = atomTypes->nextType(i1)) {
121        
122 <      // add it to the map:
123 <      AtomTypeProperties atp = atype1->getATP();    
124 <      
122 >      atype1 = *at;
123 >      atid1 = atype1->getIdent();
124 >      iHash_[atid1].resize(nTypes);
125 >      interactions_[atid1].resize(nTypes);
126 >
127 >      // add it to the map:      
128        pair<map<int,AtomType*>::iterator,bool> ret;    
129 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
129 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
130        if (ret.second == false) {
131          sprintf( painCave.errMsg,
132                   "InteractionManager already had a previous entry with ident %d\n",
133 <                 atp.ident);
133 >                 atype1->getIdent());
134          painCave.severity = OPENMD_INFO;
135          painCave.isFatal = 0;
136          simError();                
# Line 128 | Line 142 | namespace OpenMD {
142      map<int, AtomType*>::iterator it1, it2;
143      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
144        atype1 = (*it1).second;
145 +      atid1 = atype1->getIdent();
146  
147        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
148          atype2 = (*it2).second;
149 +        atid2 = atype2->getIdent();
150 +                              
151 +        iHash_[atid1][atid2] = 0;
152          
135 –        bool vdwExplicit = false;
136 –        bool metExplicit = false;
137 –        bool hbExplicit = false;
138 –                      
139 –        key = make_pair(atype1, atype2);
140 –        
153          if (atype1->isLennardJones() && atype2->isLennardJones()) {
154 <          interactions_[key].insert(lj_);
154 >          interactions_[atid1][atid2].insert(lj_);
155 >          iHash_[atid1][atid2] |= LJ_PAIR;
156          }
157          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158 <          interactions_[key].insert(electrostatic_);
158 >          interactions_[atid1][atid2].insert(electrostatic_);
159 >          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
160          }
161          if (atype1->isSticky() && atype2->isSticky() ) {
162 <          interactions_[key].insert(sticky_);
162 >          interactions_[atid1][atid2].insert(sticky_);
163 >          iHash_[atid1][atid2] |= STICKY_PAIR;
164          }
165          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166 <          interactions_[key].insert(sticky_);
166 >          interactions_[atid1][atid2].insert(sticky_);
167 >          iHash_[atid1][atid2] |= STICKY_PAIR;
168          }
169          if (atype1->isEAM() && atype2->isEAM() ) {
170 <          interactions_[key].insert(eam_);
170 >          interactions_[atid1][atid2].insert(eam_);
171 >          iHash_[atid1][atid2] |= EAM_PAIR;
172          }
173          if (atype1->isSC() && atype2->isSC() ) {
174 <          interactions_[key].insert(sc_);
174 >          interactions_[atid1][atid2].insert(sc_);
175 >          iHash_[atid1][atid2] |= SC_PAIR;
176          }
177          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178 <          interactions_[key].insert(gb_);
178 >          interactions_[atid1][atid2].insert(gb_);
179 >          iHash_[atid1][atid2] |= GB_PAIR;
180          }
181          if ((atype1->isGayBerne() && atype2->isLennardJones())
182              || (atype1->isLennardJones() && atype2->isGayBerne())) {
183 <          interactions_[key].insert(gb_);
183 >          interactions_[atid1][atid2].insert(gb_);
184 >          iHash_[atid1][atid2] |= GB_PAIR;
185          }
186          
187          // look for an explicitly-set non-bonded interaction type using the
188          // two atom types.
189          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
190 +        
191 +        if (nbiType != NULL) {
192  
193 <        if (nbiType->isLennardJones()) {
194 <          // We found an explicit Lennard-Jones interaction.  
195 <          // override all other vdw entries for this pair of atom types:
174 <          set<NonBondedInteraction*>::iterator it;
175 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
176 <            InteractionFamily ifam = (*it)->getFamily();
177 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
178 <          }
179 <          interactions_[key].insert(lj_);
180 <          vdwExplicit = true;
181 <        }
193 >          bool vdwExplicit = false;
194 >          bool metExplicit = false;
195 >          // bool hbExplicit = false;
196  
197 <        if (nbiType->isMorse()) {
198 <          if (vdwExplicit) {
199 <            sprintf( painCave.errMsg,
200 <                     "InteractionManager::initialize found more than one explicit\n"
201 <                     "\tvan der Waals interaction for atom types %s - %s\n",
202 <                     atype1->getName().c_str(), atype2->getName().c_str());
203 <            painCave.severity = OPENMD_ERROR;
204 <            painCave.isFatal = 1;
205 <            simError();
206 <          }
207 <          // We found an explicit Morse interaction.  
208 <          // override all other vdw entries for this pair of atom types:
209 <          set<NonBondedInteraction*>::iterator it;
210 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
211 <            InteractionFamily ifam = (*it)->getFamily();
198 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
199 <          }
200 <          interactions_[key].insert(morse_);
201 <          vdwExplicit = true;
202 <        }
203 <
204 <        if (nbiType->isEAM()) {
205 <          // We found an explicit EAM interaction.  
206 <          // override all other metallic entries for this pair of atom types:
207 <          set<NonBondedInteraction*>::iterator it;
208 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
209 <            InteractionFamily ifam = (*it)->getFamily();
210 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
197 >          if (nbiType->isLennardJones()) {
198 >            // We found an explicit Lennard-Jones interaction.  
199 >            // override all other vdw entries for this pair of atom types:
200 >            set<NonBondedInteraction*>::iterator it;
201 >            for (it = interactions_[atid1][atid2].begin();
202 >                 it != interactions_[atid1][atid2].end(); ++it) {
203 >              InteractionFamily ifam = (*it)->getFamily();
204 >              if (ifam == VANDERWAALS_FAMILY) {
205 >                interactions_[atid1][atid2].erase(*it);
206 >                iHash_[atid1][atid2] ^= (*it)->getHash();
207 >              }
208 >            }
209 >            interactions_[atid1][atid2].insert(lj_);
210 >            iHash_[atid1][atid2] |= LJ_PAIR;
211 >            vdwExplicit = true;
212            }
213 <          interactions_[key].insert(eam_);
214 <          metExplicit = true;
215 <        }
216 <
217 <        if (nbiType->isSC()) {
218 <          if (metExplicit) {
219 <            sprintf( painCave.errMsg,
220 <                     "InteractionManager::initialize found more than one explicit\n"
221 <                     "\tmetallic interaction for atom types %s - %s\n",
222 <                     atype1->getName().c_str(), atype2->getName().c_str());
223 <            painCave.severity = OPENMD_ERROR;
224 <            painCave.isFatal = 1;
225 <            simError();
213 >          
214 >          if (nbiType->isMorse()) {
215 >            if (vdwExplicit) {
216 >              sprintf( painCave.errMsg,
217 >                       "InteractionManager::initialize found more than one "
218 >                       "explicit \n"
219 >                       "\tvan der Waals interaction for atom types %s - %s\n",
220 >                       atype1->getName().c_str(), atype2->getName().c_str());
221 >              painCave.severity = OPENMD_ERROR;
222 >              painCave.isFatal = 1;
223 >              simError();
224 >            }
225 >            // We found an explicit Morse interaction.  
226 >            // override all other vdw entries for this pair of atom types:
227 >            set<NonBondedInteraction*>::iterator it;
228 >            for (it = interactions_[atid1][atid2].begin();
229 >                 it != interactions_[atid1][atid2].end(); ++it) {
230 >              InteractionFamily ifam = (*it)->getFamily();
231 >              if (ifam == VANDERWAALS_FAMILY) {
232 >                interactions_[atid1][atid2].erase(*it);
233 >                iHash_[atid1][atid2] ^= (*it)->getHash();
234 >              }
235 >            }
236 >            interactions_[atid1][atid2].insert(morse_);
237 >            iHash_[atid1][atid2] |= MORSE_PAIR;
238 >            vdwExplicit = true;
239            }
226 –          // We found an explicit Sutton-Chen interaction.  
227 –          // override all other metallic entries for this pair of atom types:
228 –          set<NonBondedInteraction*>::iterator it;
229 –          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
230 –            InteractionFamily ifam = (*it)->getFamily();
231 –            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
232 –          }
233 –          interactions_[key].insert(sc_);
234 –          metExplicit = true;
235 –        }
240  
241 <        if (nbiType->isMAW()) {
242 <          if (vdwExplicit) {
243 <            sprintf( painCave.errMsg,
244 <                     "InteractionManager::initialize found more than one explicit\n"
245 <                     "\tvan der Waals interaction for atom types %s - %s\n",
246 <                     atype1->getName().c_str(), atype2->getName().c_str());
247 <            painCave.severity = OPENMD_ERROR;
248 <            painCave.isFatal = 1;
249 <            simError();
241 >          if (nbiType->isRepulsivePower()) {
242 >            if (vdwExplicit) {
243 >              sprintf( painCave.errMsg,
244 >                       "InteractionManager::initialize found more than one "
245 >                       "explicit \n"
246 >                       "\tvan der Waals interaction for atom types %s - %s\n",
247 >                       atype1->getName().c_str(), atype2->getName().c_str());
248 >              painCave.severity = OPENMD_ERROR;
249 >              painCave.isFatal = 1;
250 >              simError();
251 >            }
252 >            // We found an explicit RepulsivePower interaction.  
253 >            // override all other vdw entries for this pair of atom types:
254 >            set<NonBondedInteraction*>::iterator it;
255 >            for (it = interactions_[atid1][atid2].begin();
256 >                 it != interactions_[atid1][atid2].end(); ++it) {
257 >              InteractionFamily ifam = (*it)->getFamily();
258 >              if (ifam == VANDERWAALS_FAMILY) {
259 >                interactions_[atid1][atid2].erase(*it);
260 >                iHash_[atid1][atid2] ^= (*it)->getHash();
261 >              }
262 >            }
263 >            interactions_[atid1][atid2].insert(repulsivePower_);
264 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
265 >            vdwExplicit = true;
266            }
267 <          // We found an explicit MAW interaction.  
268 <          // override all other vdw entries for this pair of atom types:
269 <          set<NonBondedInteraction*>::iterator it;
270 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
271 <            InteractionFamily ifam = (*it)->getFamily();
272 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
267 >          
268 >          
269 >          if (nbiType->isEAM()) {
270 >            // We found an explicit EAM interaction.  
271 >            // override all other metallic entries for this pair of atom types:
272 >            set<NonBondedInteraction*>::iterator it;
273 >            for (it = interactions_[atid1][atid2].begin();
274 >                 it != interactions_[atid1][atid2].end(); ++it) {
275 >              InteractionFamily ifam = (*it)->getFamily();
276 >              if (ifam == METALLIC_FAMILY) {
277 >                interactions_[atid1][atid2].erase(*it);
278 >                iHash_[atid1][atid2] ^= (*it)->getHash();
279 >              }
280 >            }
281 >            interactions_[atid1][atid2].insert(eam_);
282 >            iHash_[atid1][atid2] |= EAM_PAIR;
283 >            metExplicit = true;
284            }
285 <          interactions_[key].insert(maw_);
286 <          vdwExplicit = true;
287 <        }        
285 >          
286 >          if (nbiType->isSC()) {
287 >            if (metExplicit) {
288 >              sprintf( painCave.errMsg,
289 >                       "InteractionManager::initialize found more than one "
290 >                       "explicit\n"
291 >                       "\tmetallic interaction for atom types %s - %s\n",
292 >                       atype1->getName().c_str(), atype2->getName().c_str());
293 >              painCave.severity = OPENMD_ERROR;
294 >              painCave.isFatal = 1;
295 >              simError();
296 >            }
297 >            // We found an explicit Sutton-Chen interaction.  
298 >            // override all other metallic entries for this pair of atom types:
299 >            set<NonBondedInteraction*>::iterator it;
300 >            for (it = interactions_[atid1][atid2].begin();
301 >                 it != interactions_[atid1][atid2].end(); ++it) {
302 >              InteractionFamily ifam = (*it)->getFamily();
303 >              if (ifam == METALLIC_FAMILY) {
304 >                interactions_[atid1][atid2].erase(*it);
305 >                iHash_[atid1][atid2] ^= (*it)->getHash();
306 >              }
307 >            }
308 >            interactions_[atid1][atid2].insert(sc_);
309 >            iHash_[atid1][atid2] |= SC_PAIR;
310 >            metExplicit = true;
311 >          }
312 >          
313 >          if (nbiType->isMAW()) {
314 >            if (vdwExplicit) {
315 >              sprintf( painCave.errMsg,
316 >                       "InteractionManager::initialize found more than one "
317 >                       "explicit\n"
318 >                       "\tvan der Waals interaction for atom types %s - %s\n",
319 >                       atype1->getName().c_str(), atype2->getName().c_str());
320 >              painCave.severity = OPENMD_ERROR;
321 >              painCave.isFatal = 1;
322 >              simError();
323 >            }
324 >            // We found an explicit MAW interaction.  
325 >            // override all other vdw entries for this pair of atom types:
326 >            set<NonBondedInteraction*>::iterator it;
327 >            for (it = interactions_[atid1][atid2].begin();
328 >                 it != interactions_[atid1][atid2].end(); ++it) {
329 >              InteractionFamily ifam = (*it)->getFamily();
330 >              if (ifam == VANDERWAALS_FAMILY) {
331 >                interactions_[atid1][atid2].erase(*it);
332 >                iHash_[atid1][atid2] ^= (*it)->getHash();
333 >              }
334 >            }
335 >            interactions_[atid1][atid2].insert(maw_);
336 >            iHash_[atid1][atid2] |= MAW_PAIR;
337 >            vdwExplicit = true;
338 >          }        
339 >        }
340        }
341      }
342      
343 <    // make sure every pair of atom types has a non-bonded interaction:
344 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
345 <         atype1 = atomTypes->nextType(i1)) {
346 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
347 <           atype2 = atomTypes->nextType(i2)) {
348 <        key = make_pair(atype1, atype2);
343 >    
344 >    // Make sure every pair of atom types in this simulation has a
345 >    // non-bonded interaction.  If not, just inform the user.
346 >
347 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
348 >    set<AtomType*>::iterator it, jt;
349 >
350 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
351 >      atype1 = (*it);
352 >      atid1 = atype1->getIdent();
353 >      for (jt = it; jt != simTypes.end(); ++jt) {
354 >        atype2 = (*jt);
355 >        atid1 = atype1->getIdent();
356          
357 <        if (interactions_[key].size() == 0) {
357 >        if (interactions_[atid1][atid2].size() == 0) {
358            sprintf( painCave.errMsg,
359 <                   "InteractionManager unable to find an appropriate non-bonded\n"
360 <                   "\tinteraction for atom types %s - %s\n",
359 >                   "InteractionManager could not find a matching non-bonded\n"
360 >                   "\tinteraction for atom types %s - %s\n"
361 >                   "\tProceeding without this interaction.\n",
362                     atype1->getName().c_str(), atype2->getName().c_str());
363            painCave.severity = OPENMD_INFO;
364 <          painCave.isFatal = 1;
364 >          painCave.isFatal = 0;
365            simError();
366          }
367        }
368      }
369 <  }
370 <  
371 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
369 >
370 >    initialized_ = true;
371 >  }
372 >
373 >  void InteractionManager::setCutoffRadius(RealType rcut) {
374      
375 +    electrostatic_->setCutoffRadius(rcut);
376 +    eam_->setCutoffRadius(rcut);
377 +  }
378 +
379 +  void InteractionManager::doPrePair(InteractionData &idat){
380 +    
381      if (!initialized_) initialize();
382 <          
383 <    DensityData ddat;
382 >        
383 >    // excluded interaction, so just return
384 >    if (idat.excluded) return;
385  
386 <    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;
386 >    int& iHash = iHash_[idat.atid1][idat.atid2];
387  
388 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
389 <    set<NonBondedInteraction*>::iterator it;
388 >    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389 >    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);
390  
391 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
392 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
393 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
394 <      }
395 <    }
391 >    // set<NonBondedInteraction*>::iterator it;
392 >
393 >    // for (it = interactions_[ idat.atypes ].begin();
394 >    //      it != interactions_[ idat.atypes ].end(); ++it){
395 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
396 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
397 >    //   }
398 >    // }
399      
400      return;    
401    }
402    
403 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
403 >  void InteractionManager::doPreForce(SelfData &sdat){
404  
405      if (!initialized_) initialize();
406 <          
407 <    FunctionalData fdat;
406 >    
407 >    int& iHash = iHash_[sdat.atid][sdat.atid];
408  
409 <    fdat.atype = typeMap_[*atid];
410 <    fdat.rho = *rho;
312 <    fdat.frho = *frho;
313 <    fdat.dfrhodrho = *dfrhodrho;
409 >    if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
410 >    if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);
411  
412 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
316 <    set<NonBondedInteraction*>::iterator it;
412 >    // set<NonBondedInteraction*>::iterator it;
413      
414 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
415 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
416 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
417 <      }
418 <    }
414 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
415 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417 >    //   }
418 >    // }
419      
420      return;    
421    }
422  
423 <  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){
423 >  void InteractionManager::doPair(InteractionData &idat){
424      
425      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;
426  
427 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
359 <    set<NonBondedInteraction*>::iterator it;
427 >    int& iHash = iHash_[idat.atid1][idat.atid2];
428  
429 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
430 <      (*it)->calcForce(idat);
431 <    
432 <    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();
429 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430 >      
431 >    // electrostatics still has to worry about indirect
432 >    // contributions from excluded pairs of atoms, but nothing else does:
433  
434 <    return;    
377 <  }
434 >    if (idat.excluded) return;
435  
436 <  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){
436 >    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
437 >    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
438 >    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
439 >    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
440 >    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
441 >    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
442 >    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
443 >    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);
444  
445 <    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);
445 >    // set<NonBondedInteraction*>::iterator it;
446  
447 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
448 <    set<NonBondedInteraction*>::iterator it;
447 >    // for (it = interactions_[ idat.atypes ].begin();
448 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
449  
450 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
451 <      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();
450 >    //   // electrostatics still has to worry about indirect
451 >    //   // contributions from excluded pairs of atoms:
452  
453 +    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
454 +    //     (*it)->calcForce(idat);
455 +    //   }
456 +    // }
457 +    
458      return;    
459    }
460  
461 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
461 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
462  
463      if (!initialized_) initialize();
464      
465 <    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);
465 >    int& iHash = iHash_[sdat.atid][sdat.atid];
466  
467 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
438 <    set<NonBondedInteraction*>::iterator it;
467 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468  
469 <    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();
469 >    // set<NonBondedInteraction*>::iterator it;
470  
471 +    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
472 +    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 +    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
474 +    //   }
475 +    // }
476 +      
477      return;    
478    }
479  
480 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
481 +    if (!initialized_) initialize();
482 +    electrostatic_->ReciprocalSpaceSum(pot);
483 +  }
484  
485    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
486      if (!initialized_) initialize();
487 <    
487 >
488      AtomType* atype = typeMap_[*atid];
489  
459 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
490      set<NonBondedInteraction*>::iterator it;
491      RealType cutoff = 0.0;
492      
493 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
494 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
493 >    for (it = interactions_[*atid][*atid].begin();
494 >         it != interactions_[*atid][*atid].end();
495 >         ++it)
496 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
497      return cutoff;    
498    }
499  
500    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
501      if (!initialized_) initialize();
502      
503 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
503 >    int atid = atype->getIdent();
504 >
505      set<NonBondedInteraction*>::iterator it;
506      RealType cutoff = 0.0;
507      
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
509 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
508 >    for (it = interactions_[atid][atid].begin();
509 >         it != interactions_[atid][atid].end(); ++it)
510 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
511      return cutoff;    
512    }
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 –
513   } //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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