ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
(Generate patch)

Comparing:
branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 2033 by gezelter, Sat Nov 1 14:12:16 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 <
55 <  InteractionManager* InteractionManager::Instance() {
56 <    if (!_instance) {
57 <      _instance = new InteractionManager();
58 <    }
59 <    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 74 | 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  
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
102 >    // simulation:
103      
104 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
105 <         atype1 = atomTypes->nextType(i1)) {
106 <      
107 <      // add it to the map:
108 <      AtomTypeProperties atp = atype1->getATP();    
109 <      
104 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
105 >
106 >    lj_->setSimulatedAtomTypes(atypes);
107 >    gb_->setSimulatedAtomTypes(atypes);
108 >    sticky_->setSimulatedAtomTypes(atypes);
109 >    eam_->setSimulatedAtomTypes(atypes);
110 >    sc_->setSimulatedAtomTypes(atypes);
111 >    morse_->setSimulatedAtomTypes(atypes);
112 >    electrostatic_->setSimInfo(info_);
113 >    electrostatic_->setSimulatedAtomTypes(atypes);
114 >    maw_->setSimulatedAtomTypes(atypes);
115 >    repulsivePower_->setSimulatedAtomTypes(atypes);
116 >
117 >    set<AtomType*>::iterator at;
118 >
119 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
120 >          
121 >      atype1 = *at;
122 >      atid1 = atype1->getIdent();
123 >      iHash_[atid1].resize(nTypes);
124 >      interactions_[atid1].resize(nTypes);
125 >
126 >      // add it to the map:      
127        pair<map<int,AtomType*>::iterator,bool> ret;    
128 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
128 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
129        if (ret.second == false) {
130          sprintf( painCave.errMsg,
131                   "InteractionManager already had a previous entry with ident %d\n",
132 <                 atp.ident);
132 >                 atype1->getIdent());
133          painCave.severity = OPENMD_INFO;
134          painCave.isFatal = 0;
135          simError();                
136        }
137 +          
138 +      if (atype1->isLennardJones()) {
139 +        sHash_[atid1] |= LJ_INTERACTION;
140 +      }
141 +      if (atype1->isElectrostatic()) {
142 +        sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
143 +      }
144 +      if (atype1->isSticky()) {
145 +        sHash_[atid1] |= STICKY_INTERACTION;
146 +      }
147 +      if (atype1->isStickyPower()) {
148 +        sHash_[atid1] |= STICKY_INTERACTION;
149 +      }
150 +      if (atype1->isEAM()) {      
151 +        sHash_[atid1] |= EAM_INTERACTION;
152 +      }
153 +      if (atype1->isSC()) {
154 +        sHash_[atid1] |= SC_INTERACTION;
155 +      }
156 +      if (atype1->isGayBerne()) {
157 +        sHash_[atid1] |= GB_INTERACTION;
158 +      }
159      }
103 –    
160      // Now, iterate over all known types and add to the interaction map:
161      
162      map<int, AtomType*>::iterator it1, it2;
163      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
164        atype1 = (*it1).second;
165 +      atid1 = atype1->getIdent();
166  
167        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
168          atype2 = (*it2).second;
169 +        atid2 = atype2->getIdent();
170 +                              
171 +        iHash_[atid1][atid2] = 0;
172          
113 –        bool vdwExplicit = false;
114 –        bool metExplicit = false;
115 –        bool hbExplicit = false;
116 –                      
117 –        key = make_pair(atype1, atype2);
118 –        
173          if (atype1->isLennardJones() && atype2->isLennardJones()) {
174 <          interactions_[key].insert(lj_);
174 >          interactions_[atid1][atid2].insert(lj_);
175 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
176          }
177          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
178 <          interactions_[key].insert(electrostatic_);
178 >          interactions_[atid1][atid2].insert(electrostatic_);
179 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
180          }
181          if (atype1->isSticky() && atype2->isSticky() ) {
182 <          interactions_[key].insert(sticky_);
182 >          interactions_[atid1][atid2].insert(sticky_);
183 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
184          }
185          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
186 <          interactions_[key].insert(sticky_);
186 >          interactions_[atid1][atid2].insert(sticky_);
187 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
188          }
189          if (atype1->isEAM() && atype2->isEAM() ) {
190 <          interactions_[key].insert(eam_);
190 >          interactions_[atid1][atid2].insert(eam_);
191 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
192          }
193          if (atype1->isSC() && atype2->isSC() ) {
194 <          interactions_[key].insert(sc_);
194 >          interactions_[atid1][atid2].insert(sc_);
195 >          iHash_[atid1][atid2] |= SC_INTERACTION;
196          }
197          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
198 <          interactions_[key].insert(gb_);
198 >          interactions_[atid1][atid2].insert(gb_);
199 >          iHash_[atid1][atid2] |= GB_INTERACTION;
200          }
201          if ((atype1->isGayBerne() && atype2->isLennardJones())
202              || (atype1->isLennardJones() && atype2->isGayBerne())) {
203 <          interactions_[key].insert(gb_);
203 >          interactions_[atid1][atid2].insert(gb_);
204 >          iHash_[atid1][atid2] |= GB_INTERACTION;
205          }
206          
207          // look for an explicitly-set non-bonded interaction type using the
208          // two atom types.
209          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
210 +        
211 +        if (nbiType != NULL) {
212  
213 <        if (nbiType->isLennardJones()) {
214 <          // We found an explicit Lennard-Jones interaction.  
215 <          // override all other vdw entries for this pair of atom types:
152 <          set<NonBondedInteraction*>::iterator it;
153 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
154 <            InteractionFamily ifam = (*it)->getFamily();
155 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
156 <          }
157 <          interactions_[key].insert(lj_);
158 <          vdwExplicit = true;
159 <        }
213 >          bool vdwExplicit = false;
214 >          bool metExplicit = false;
215 >          // bool hbExplicit = false;
216  
217 <        if (nbiType->isMorse()) {
218 <          if (vdwExplicit) {
219 <            sprintf( painCave.errMsg,
220 <                     "InteractionManager::initialize found more than one explicit\n"
221 <                     "\tvan der Waals 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();
217 >          if (nbiType->isLennardJones()) {
218 >            // We found an explicit Lennard-Jones interaction.  
219 >            // override all other vdw entries for this pair of atom types:
220 >            set<NonBondedInteraction*>::iterator it;
221 >            for (it = interactions_[atid1][atid2].begin();
222 >                 it != interactions_[atid1][atid2].end(); ++it) {
223 >              InteractionFamily ifam = (*it)->getFamily();
224 >              if (ifam == VANDERWAALS_FAMILY) {
225 >                interactions_[atid1][atid2].erase(*it);
226 >                iHash_[atid1][atid2] ^= (*it)->getHash();
227 >              }
228 >            }
229 >            interactions_[atid1][atid2].insert(lj_);
230 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
231 >            vdwExplicit = true;
232            }
233 <          // We found an explicit Morse interaction.  
234 <          // override all other vdw entries for this pair of atom types:
235 <          set<NonBondedInteraction*>::iterator it;
236 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
237 <            InteractionFamily ifam = (*it)->getFamily();
238 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
233 >          
234 >          if (nbiType->isMorse()) {
235 >            if (vdwExplicit) {
236 >              sprintf( painCave.errMsg,
237 >                       "InteractionManager::initialize found more than one "
238 >                       "explicit \n"
239 >                       "\tvan der Waals interaction for atom types %s - %s\n",
240 >                       atype1->getName().c_str(), atype2->getName().c_str());
241 >              painCave.severity = OPENMD_ERROR;
242 >              painCave.isFatal = 1;
243 >              simError();
244 >            }
245 >            // We found an explicit Morse interaction.  
246 >            // override all other vdw entries for this pair of atom types:
247 >            set<NonBondedInteraction*>::iterator it;
248 >            for (it = interactions_[atid1][atid2].begin();
249 >                 it != interactions_[atid1][atid2].end(); ++it) {
250 >              InteractionFamily ifam = (*it)->getFamily();
251 >              if (ifam == VANDERWAALS_FAMILY) {
252 >                interactions_[atid1][atid2].erase(*it);
253 >                iHash_[atid1][atid2] ^= (*it)->getHash();
254 >              }
255 >            }
256 >            interactions_[atid1][atid2].insert(morse_);
257 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
258 >            vdwExplicit = true;
259            }
178 –          interactions_[key].insert(morse_);
179 –          vdwExplicit = true;
180 –        }
260  
261 <        if (nbiType->isEAM()) {
262 <          // We found an explicit EAM interaction.  
263 <          // override all other metallic entries for this pair of atom types:
264 <          set<NonBondedInteraction*>::iterator it;
265 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
266 <            InteractionFamily ifam = (*it)->getFamily();
267 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
261 >          if (nbiType->isRepulsivePower()) {
262 >            if (vdwExplicit) {
263 >              sprintf( painCave.errMsg,
264 >                       "InteractionManager::initialize found more than one "
265 >                       "explicit \n"
266 >                       "\tvan der Waals interaction for atom types %s - %s\n",
267 >                       atype1->getName().c_str(), atype2->getName().c_str());
268 >              painCave.severity = OPENMD_ERROR;
269 >              painCave.isFatal = 1;
270 >              simError();
271 >            }
272 >            // We found an explicit RepulsivePower interaction.  
273 >            // override all other vdw entries for this pair of atom types:
274 >            set<NonBondedInteraction*>::iterator it;
275 >            for (it = interactions_[atid1][atid2].begin();
276 >                 it != interactions_[atid1][atid2].end(); ++it) {
277 >              InteractionFamily ifam = (*it)->getFamily();
278 >              if (ifam == VANDERWAALS_FAMILY) {
279 >                interactions_[atid1][atid2].erase(*it);
280 >                iHash_[atid1][atid2] ^= (*it)->getHash();
281 >              }
282 >            }
283 >            interactions_[atid1][atid2].insert(repulsivePower_);
284 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
285 >            vdwExplicit = true;
286            }
287 <          interactions_[key].insert(eam_);
288 <          metExplicit = true;
289 <        }
290 <
291 <        if (nbiType->isSC()) {
292 <          if (metExplicit) {
293 <            sprintf( painCave.errMsg,
294 <                     "InteractionManager::initialize found more than one explicit\n"
295 <                     "\tmetallic interaction for atom types %s - %s\n",
296 <                     atype1->getName().c_str(), atype2->getName().c_str());
297 <            painCave.severity = OPENMD_ERROR;
298 <            painCave.isFatal = 1;
299 <            simError();
287 >          
288 >          
289 >          if (nbiType->isEAM()) {
290 >            // We found an explicit EAM interaction.  
291 >            // override all other metallic entries for this pair of atom types:
292 >            set<NonBondedInteraction*>::iterator it;
293 >            for (it = interactions_[atid1][atid2].begin();
294 >                 it != interactions_[atid1][atid2].end(); ++it) {
295 >              InteractionFamily ifam = (*it)->getFamily();
296 >              if (ifam == METALLIC_FAMILY) {
297 >                interactions_[atid1][atid2].erase(*it);
298 >                iHash_[atid1][atid2] ^= (*it)->getHash();
299 >              }
300 >            }
301 >            interactions_[atid1][atid2].insert(eam_);
302 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
303 >            metExplicit = true;
304            }
305 <          // We found an explicit Sutton-Chen interaction.  
306 <          // override all other metallic entries for this pair of atom types:
307 <          set<NonBondedInteraction*>::iterator it;
308 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
309 <            InteractionFamily ifam = (*it)->getFamily();
310 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
305 >          
306 >          if (nbiType->isSC()) {
307 >            if (metExplicit) {
308 >              sprintf( painCave.errMsg,
309 >                       "InteractionManager::initialize found more than one "
310 >                       "explicit\n"
311 >                       "\tmetallic interaction for atom types %s - %s\n",
312 >                       atype1->getName().c_str(), atype2->getName().c_str());
313 >              painCave.severity = OPENMD_ERROR;
314 >              painCave.isFatal = 1;
315 >              simError();
316 >            }
317 >            // We found an explicit Sutton-Chen interaction.  
318 >            // override all other metallic entries for this pair of atom types:
319 >            set<NonBondedInteraction*>::iterator it;
320 >            for (it = interactions_[atid1][atid2].begin();
321 >                 it != interactions_[atid1][atid2].end(); ++it) {
322 >              InteractionFamily ifam = (*it)->getFamily();
323 >              if (ifam == METALLIC_FAMILY) {
324 >                interactions_[atid1][atid2].erase(*it);
325 >                iHash_[atid1][atid2] ^= (*it)->getHash();
326 >              }
327 >            }
328 >            interactions_[atid1][atid2].insert(sc_);
329 >            iHash_[atid1][atid2] |= SC_INTERACTION;
330 >            metExplicit = true;
331            }
332 <          interactions_[key].insert(sc_);
333 <          metExplicit = true;
332 >          
333 >          if (nbiType->isMAW()) {
334 >            if (vdwExplicit) {
335 >              sprintf( painCave.errMsg,
336 >                       "InteractionManager::initialize found more than one "
337 >                       "explicit\n"
338 >                       "\tvan der Waals interaction for atom types %s - %s\n",
339 >                       atype1->getName().c_str(), atype2->getName().c_str());
340 >              painCave.severity = OPENMD_ERROR;
341 >              painCave.isFatal = 1;
342 >              simError();
343 >            }
344 >            // We found an explicit MAW interaction.  
345 >            // override all other vdw entries for this pair of atom types:
346 >            set<NonBondedInteraction*>::iterator it;
347 >            for (it = interactions_[atid1][atid2].begin();
348 >                 it != interactions_[atid1][atid2].end(); ++it) {
349 >              InteractionFamily ifam = (*it)->getFamily();
350 >              if (ifam == VANDERWAALS_FAMILY) {
351 >                interactions_[atid1][atid2].erase(*it);
352 >                iHash_[atid1][atid2] ^= (*it)->getHash();
353 >              }
354 >            }
355 >            interactions_[atid1][atid2].insert(maw_);
356 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
357 >            vdwExplicit = true;
358 >          }        
359          }
360        }
361      }
362      
363 <    // make sure every pair of atom types has a non-bonded interaction:
364 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
365 <         atype1 = atomTypes->nextType(i1)) {
366 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
367 <           atype2 = atomTypes->nextType(i2)) {
368 <        key = make_pair(atype1, atype2);
363 >    
364 >    // Make sure every pair of atom types in this simulation has a
365 >    // non-bonded interaction.  If not, just inform the user.
366 >
367 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
368 >    set<AtomType*>::iterator it, jt;
369 >
370 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
371 >      atype1 = (*it);
372 >      atid1 = atype1->getIdent();
373 >      for (jt = it; jt != simTypes.end(); ++jt) {
374 >        atype2 = (*jt);
375 >        atid2 = atype2->getIdent();
376          
377 <        if (interactions_[key].size() == 0) {
377 >        if (interactions_[atid1][atid2].size() == 0) {
378            sprintf( painCave.errMsg,
379 <                   "InteractionManager unable to find an appropriate non-bonded\n"
380 <                   "\tinteraction for atom types %s - %s\n",
379 >                   "InteractionManager could not find a matching non-bonded\n"
380 >                   "\tinteraction for atom types %s - %s\n"
381 >                   "\tProceeding without this interaction.\n",
382                     atype1->getName().c_str(), atype2->getName().c_str());
383            painCave.severity = OPENMD_INFO;
384 <          painCave.isFatal = 1;
384 >          painCave.isFatal = 0;
385            simError();
386          }
387        }
388      }
389 <  }
390 <  
391 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
389 >
390 >    initialized_ = true;
391 >  }
392 >
393 >  void InteractionManager::setCutoffRadius(RealType rcut) {
394      
395 +    electrostatic_->setCutoffRadius(rcut);
396 +    eam_->setCutoffRadius(rcut);
397 +  }
398 +
399 +  void InteractionManager::doPrePair(InteractionData &idat){
400 +    
401      if (!initialized_) initialize();
402 <          
403 <    DensityData ddat;
402 >        
403 >    // excluded interaction, so just return
404 >    if (idat.excluded) return;
405  
406 <    ddat.atype1 = typeMap_[*atid1];
244 <    ddat.atype2 = typeMap_[*atid2];
245 <    ddat.rij = *rij;
246 <    ddat.rho_i_at_j = *rho_i_at_j;
247 <    ddat.rho_j_at_i = *rho_j_at_i;
406 >    int& iHash = iHash_[idat.atid1][idat.atid2];
407  
408 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
409 <    set<NonBondedInteraction*>::iterator it;
408 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
409 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
410  
411 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
412 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
413 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
414 <      }
415 <    }
411 >    // set<NonBondedInteraction*>::iterator it;
412 >
413 >    // for (it = interactions_[ idat.atypes ].begin();
414 >    //      it != interactions_[ idat.atypes ].end(); ++it){
415 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
417 >    //   }
418 >    // }
419      
420      return;    
421    }
422    
423 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
423 >  void InteractionManager::doPreForce(SelfData &sdat){
424  
425      if (!initialized_) initialize();
426 <          
427 <    FunctionalData fdat;
426 >    
427 >    int& sHash = sHash_[sdat.atid];
428  
429 <    fdat.atype = typeMap_[*atid];
430 <    fdat.rho = *rho;
269 <    fdat.frho = *frho;
270 <    fdat.dfrhodrho = *dfrhodrho;
429 >    if ((sHash & EAM_INTERACTION) != 0)  eam_->calcFunctional(sdat);
430 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
431  
432 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
273 <    set<NonBondedInteraction*>::iterator it;
432 >    // set<NonBondedInteraction*>::iterator it;
433      
434 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
435 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
436 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
437 <      }
438 <    }
434 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
435 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
436 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
437 >    //   }
438 >    // }
439      
440      return;    
441    }
442  
443 <  void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult,RealType *electroMult, 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){
443 >  void InteractionManager::doPair(InteractionData &idat){
444      
445      if (!initialized_) initialize();
287 –    
288 –    InteractionData idat;
289 –    
290 –    idat.atype1 = typeMap_[*atid1];
291 –    idat.atype2 = typeMap_[*atid2];
292 –    idat.d = Vector3d(d);
293 –    idat.rij = *r;
294 –    idat.r2 = *r2;
295 –    idat.rcut = *rcut;
296 –    idat.sw = *sw;
297 –    idat.vdwMult = *vdwMult;
298 –    idat.electroMult = *electroMult;
299 –    idat.pot = *pot;
300 –    idat.vpair = *vpair;
301 –    idat.f1 = Vector3d(f1);
302 –    idat.eFrame1 = Mat3x3d(eFrame1);
303 –    idat.eFrame2 = Mat3x3d(eFrame2);
304 –    idat.A1 = RotMat3x3d(A1);
305 –    idat.A2 = RotMat3x3d(A2);
306 –    idat.t1 = Vector3d(t1);
307 –    idat.t2 = Vector3d(t2);
308 –    idat.rho1 = *rho1;
309 –    idat.rho2 = *rho2;
310 –    idat.dfrho1 = *dfrho1;
311 –    idat.dfrho2 = *dfrho2;
312 –    idat.fshift1 = *fshift1;
313 –    idat.fshift2 = *fshift2;
446  
447 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
316 <    set<NonBondedInteraction*>::iterator it;
447 >    int& iHash = iHash_[idat.atid1][idat.atid2];
448  
449 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
450 <      (*it)->calcForce(idat);
451 <    
452 <    f1[0] = idat.f1.x();
322 <    f1[1] = idat.f1.y();
323 <    f1[2] = idat.f1.z();
324 <    
325 <    t1[0] = idat.t1.x();
326 <    t1[1] = idat.t1.y();
327 <    t1[2] = idat.t1.z();
328 <    
329 <    t2[0] = idat.t2.x();
330 <    t2[1] = idat.t2.y();
331 <    t2[2] = idat.t2.z();
449 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
450 >      
451 >    // electrostatics still has to worry about indirect
452 >    // contributions from excluded pairs of atoms, but nothing else does:
453  
454 <    return;    
334 <  }
454 >    if (idat.excluded) return;
455  
456 <  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){
456 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
457 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
458 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
459 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
460 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
461 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
462 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
463 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
464  
465 <    if (!initialized_) initialize();
339 <    
340 <    SkipCorrectionData skdat;
341 <    
342 <    skdat.atype1 = typeMap_[*atid1];
343 <    skdat.atype2 = typeMap_[*atid2];
344 <    skdat.d = Vector3d(d);
345 <    skdat.rij = *r;
346 <    skdat.skippedCharge1 = *skippedCharge1;
347 <    skdat.skippedCharge2 = *skippedCharge2;
348 <    skdat.sw = *sw;
349 <    skdat.electroMult = *electroMult;
350 <    skdat.pot = *pot;
351 <    skdat.vpair = *vpair;
352 <    skdat.f1 = Vector3d(f1);
353 <    skdat.eFrame1 = Mat3x3d(eFrame1);
354 <    skdat.eFrame2 = Mat3x3d(eFrame2);
355 <    skdat.t1 = Vector3d(t1);
356 <    skdat.t2 = Vector3d(t2);
465 >    // set<NonBondedInteraction*>::iterator it;
466  
467 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
468 <    set<NonBondedInteraction*>::iterator it;
467 >    // for (it = interactions_[ idat.atypes ].begin();
468 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
469  
470 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
471 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
363 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
364 <      }
365 <    }
366 <    
367 <    f1[0] = skdat.f1.x();
368 <    f1[1] = skdat.f1.y();
369 <    f1[2] = skdat.f1.z();
370 <    
371 <    t1[0] = skdat.t1.x();
372 <    t1[1] = skdat.t1.y();
373 <    t1[2] = skdat.t1.z();
374 <    
375 <    t2[0] = skdat.t2.x();
376 <    t2[1] = skdat.t2.y();
377 <    t2[2] = skdat.t2.z();
470 >    //   // electrostatics still has to worry about indirect
471 >    //   // contributions from excluded pairs of atoms:
472  
473 +    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
474 +    //     (*it)->calcForce(idat);
475 +    //   }
476 +    // }
477 +    
478      return;    
479    }
480  
481 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
481 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
482  
483      if (!initialized_) initialize();
484      
485 <    SelfCorrectionData scdat;
387 <    
388 <    scdat.atype = typeMap_[*atid];
389 <    scdat.eFrame = Mat3x3d(eFrame);
390 <    scdat.skippedCharge = *skippedCharge;
391 <    scdat.pot = *pot;
392 <    scdat.t = Vector3d(t);
485 >    int& sHash = sHash_[sdat.atid];
486  
487 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
395 <    set<NonBondedInteraction*>::iterator it;
487 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
488  
489 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
398 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
399 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
400 <      }
401 <    }
402 <        
403 <    t[0] = scdat.t.x();
404 <    t[1] = scdat.t.y();
405 <    t[2] = scdat.t.z();
489 >    // set<NonBondedInteraction*>::iterator it;
490  
491 +    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
492 +    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
493 +    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
494 +    //   }
495 +    // }
496 +      
497      return;    
498    }
499  
500 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
501 +    if (!initialized_) initialize();
502 +    electrostatic_->ReciprocalSpaceSum(pot);
503 +  }
504  
505    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
506      if (!initialized_) initialize();
507 <    
507 >
508      AtomType* atype = typeMap_[*atid];
509  
416 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
510      set<NonBondedInteraction*>::iterator it;
511      RealType cutoff = 0.0;
512      
513 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
514 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
513 >    for (it = interactions_[*atid][*atid].begin();
514 >         it != interactions_[*atid][*atid].end();
515 >         ++it)
516 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
517 >                                                                     atype)));
518      return cutoff;    
519    }
520  
521    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
522      if (!initialized_) initialize();
523      
524 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
524 >    int atid = atype->getIdent();
525 >
526      set<NonBondedInteraction*>::iterator it;
527      RealType cutoff = 0.0;
528      
529 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
530 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
529 >    for (it = interactions_[atid][atid].begin();
530 >         it != interactions_[atid][atid].end(); ++it)
531 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
532 >                                                                     atype)));
533      return cutoff;    
534    }
436 –
535   } //end namespace OpenMD
438 –
439 – extern "C" {
440 –  
441 – #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
442 – #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
443 – #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
444 – #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
445 – #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
446 – #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
447 –
448 –  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
449 –                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
450 –            
451 –    return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij,
452 –                                                             rho_i_at_j,  
453 –                                                             rho_j_at_i);
454 –  }
455 –  void fortranDoPreForce(int *atid, RealType *rho, RealType *frho,
456 –                         RealType *dfrhodrho) {  
457 –    
458 –    return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho,
459 –                                                              dfrhodrho);    
460 –  }
461 –  
462 –  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r,
463 –                     RealType *r2, RealType *rcut, RealType *sw,
464 –                     RealType *vdwMult, RealType *electroMult, RealType *pot,
465 –                     RealType *vpair, RealType *f1, RealType *eFrame1,
466 –                     RealType *eFrame2, RealType *A1, RealType *A2,
467 –                     RealType *t1, RealType *t2, RealType *rho1, RealType *rho2,
468 –                     RealType *dfrho1, RealType *dfrho2, RealType *fshift1,
469 –                     RealType *fshift2){
470 –    
471 –    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r,
472 –                                                          r2, rcut, sw,
473 –                                                          vdwMult, electroMult,
474 –                                                          pot, vpair, f1,
475 –                                                          eFrame1, eFrame2,
476 –                                                          A1, A2, t1, t2, rho1,
477 –                                                          rho2, dfrho1, dfrho2,
478 –                                                          fshift1, fshift2);
479 –  }
480 –  
481 –  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d,
482 –                               RealType *r, RealType *skippedCharge1,
483 –                               RealType *skippedCharge2, RealType *sw,
484 –                               RealType *electroMult, RealType *pot,
485 –                               RealType *vpair, RealType *f1,
486 –                               RealType *eFrame1, RealType *eFrame2,
487 –                               RealType *t1, RealType *t2){
488 –    
489 –    return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1,
490 –                                                                    atid2, d,
491 –                                                                    r,
492 –                                                                    skippedCharge1,
493 –                                                                    skippedCharge2,
494 –                                                                    sw, electroMult, pot,
495 –                                                                    vpair, f1, eFrame1,
496 –                                                                    eFrame2, t1, t2);
497 –  }
498 –  
499 –  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
500 –                               RealType *pot, RealType *t) {
501 –    
502 –    return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid,
503 –                                                                    eFrame,
504 –                                                                    skippedCharge,
505 –                                                                    pot, t);
506 –  }
507 –  RealType fortranGetCutoff(int *atid) {    
508 –    return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid);
509 –  }
510 – }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines