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Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "nonbonded/InteractionManager.hpp"
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    void InteractionManager::initialize() {
63 +
64 +    if (initialized_) return;
65 +
66 +    ForceField* forceField_ = info_->getForceField();
67      
68      lj_->setForceField(forceField_);
69      gb_->setForceField(forceField_);
# Line 76 | Line 71 | namespace OpenMD {
71      eam_->setForceField(forceField_);
72      sc_->setForceField(forceField_);
73      morse_->setForceField(forceField_);
74 +    electrostatic_->setSimInfo(info_);
75      electrostatic_->setForceField(forceField_);
76      maw_->setForceField(forceField_);
77 +    repulsivePower_->setForceField(forceField_);
78  
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 –
79      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
80      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
81      AtomType* atype1;
# Line 109 | Line 87 | namespace OpenMD {
87           atype1 = atomTypes->nextType(i1)) {
88        
89        // add it to the map:
112 –      AtomTypeProperties atp = atype1->getATP();    
90        
91        pair<map<int,AtomType*>::iterator,bool> ret;    
92 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
92 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
93        if (ret.second == false) {
94          sprintf( painCave.errMsg,
95                   "InteractionManager already had a previous entry with ident %d\n",
96 <                 atp.ident);
96 >                 atype1->getIdent());
97          painCave.severity = OPENMD_INFO;
98          painCave.isFatal = 0;
99          simError();                
# Line 134 | Line 111 | namespace OpenMD {
111          
112          bool vdwExplicit = false;
113          bool metExplicit = false;
114 <        bool hbExplicit = false;
114 >        // bool hbExplicit = false;
115                        
116          key = make_pair(atype1, atype2);
117          
# Line 167 | Line 144 | namespace OpenMD {
144          // look for an explicitly-set non-bonded interaction type using the
145          // two atom types.
146          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
147 +        
148 +        if (nbiType != NULL) {
149  
150 <        if (nbiType->isLennardJones()) {
151 <          // We found an explicit Lennard-Jones interaction.  
152 <          // override all other vdw entries for this pair of atom types:
153 <          set<NonBondedInteraction*>::iterator it;
154 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
155 <            InteractionFamily ifam = (*it)->getFamily();
156 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
150 >          if (nbiType->isLennardJones()) {
151 >            // We found an explicit Lennard-Jones interaction.  
152 >            // override all other vdw entries for this pair of atom types:
153 >            set<NonBondedInteraction*>::iterator it;
154 >            for (it = interactions_[key].begin();
155 >                 it != interactions_[key].end(); ++it) {
156 >              InteractionFamily ifam = (*it)->getFamily();
157 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
158 >            }
159 >            interactions_[key].insert(lj_);
160 >            vdwExplicit = true;
161            }
162 <          interactions_[key].insert(lj_);
163 <          vdwExplicit = true;
164 <        }
165 <
166 <        if (nbiType->isMorse()) {
167 <          if (vdwExplicit) {
168 <            sprintf( painCave.errMsg,
169 <                     "InteractionManager::initialize found more than one explicit\n"
170 <                     "\tvan der Waals interaction for atom types %s - %s\n",
171 <                     atype1->getName().c_str(), atype2->getName().c_str());
172 <            painCave.severity = OPENMD_ERROR;
173 <            painCave.isFatal = 1;
174 <            simError();
162 >          
163 >          if (nbiType->isMorse()) {
164 >            if (vdwExplicit) {
165 >              sprintf( painCave.errMsg,
166 >                       "InteractionManager::initialize found more than one "
167 >                       "explicit \n"
168 >                       "\tvan der Waals interaction for atom types %s - %s\n",
169 >                       atype1->getName().c_str(), atype2->getName().c_str());
170 >              painCave.severity = OPENMD_ERROR;
171 >              painCave.isFatal = 1;
172 >              simError();
173 >            }
174 >            // We found an explicit Morse interaction.  
175 >            // override all other vdw entries for this pair of atom types:
176 >            set<NonBondedInteraction*>::iterator it;
177 >            for (it = interactions_[key].begin();
178 >                 it != interactions_[key].end(); ++it) {
179 >              InteractionFamily ifam = (*it)->getFamily();
180 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
181 >            }
182 >            interactions_[key].insert(morse_);
183 >            vdwExplicit = true;
184            }
193 –          // We found an explicit Morse interaction.  
194 –          // override all other vdw entries for this pair of atom types:
195 –          set<NonBondedInteraction*>::iterator it;
196 –          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
197 –            InteractionFamily ifam = (*it)->getFamily();
198 –            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
199 –          }
200 –          interactions_[key].insert(morse_);
201 –          vdwExplicit = true;
202 –        }
185  
186 <        if (nbiType->isEAM()) {
187 <          // We found an explicit EAM interaction.  
188 <          // override all other metallic entries for this pair of atom types:
189 <          set<NonBondedInteraction*>::iterator it;
190 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
191 <            InteractionFamily ifam = (*it)->getFamily();
192 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
186 >          if (nbiType->isRepulsivePower()) {
187 >            if (vdwExplicit) {
188 >              sprintf( painCave.errMsg,
189 >                       "InteractionManager::initialize found more than one "
190 >                       "explicit \n"
191 >                       "\tvan der Waals interaction for atom types %s - %s\n",
192 >                       atype1->getName().c_str(), atype2->getName().c_str());
193 >              painCave.severity = OPENMD_ERROR;
194 >              painCave.isFatal = 1;
195 >              simError();
196 >            }
197 >            // We found an explicit RepulsivePower interaction.  
198 >            // override all other vdw entries for this pair of atom types:
199 >            set<NonBondedInteraction*>::iterator it;
200 >            for (it = interactions_[key].begin();
201 >                 it != interactions_[key].end(); ++it) {
202 >              InteractionFamily ifam = (*it)->getFamily();
203 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 >            }
205 >            interactions_[key].insert(repulsivePower_);
206 >            vdwExplicit = true;
207            }
208 <          interactions_[key].insert(eam_);
209 <          metExplicit = true;
210 <        }
211 <
212 <        if (nbiType->isSC()) {
213 <          if (metExplicit) {
214 <            sprintf( painCave.errMsg,
215 <                     "InteractionManager::initialize found more than one explicit\n"
216 <                     "\tmetallic interaction for atom types %s - %s\n",
217 <                     atype1->getName().c_str(), atype2->getName().c_str());
218 <            painCave.severity = OPENMD_ERROR;
219 <            painCave.isFatal = 1;
220 <            simError();
208 >          
209 >          
210 >          if (nbiType->isEAM()) {
211 >            // We found an explicit EAM interaction.  
212 >            // override all other metallic entries for this pair of atom types:
213 >            set<NonBondedInteraction*>::iterator it;
214 >            for (it = interactions_[key].begin();
215 >                 it != interactions_[key].end(); ++it) {
216 >              InteractionFamily ifam = (*it)->getFamily();
217 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
218 >            }
219 >            interactions_[key].insert(eam_);
220 >            metExplicit = true;
221            }
222 <          // We found an explicit Sutton-Chen interaction.  
223 <          // override all other metallic entries for this pair of atom types:
224 <          set<NonBondedInteraction*>::iterator it;
225 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
226 <            InteractionFamily ifam = (*it)->getFamily();
227 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
222 >          
223 >          if (nbiType->isSC()) {
224 >            if (metExplicit) {
225 >              sprintf( painCave.errMsg,
226 >                       "InteractionManager::initialize found more than one "
227 >                       "explicit\n"
228 >                       "\tmetallic interaction for atom types %s - %s\n",
229 >                       atype1->getName().c_str(), atype2->getName().c_str());
230 >              painCave.severity = OPENMD_ERROR;
231 >              painCave.isFatal = 1;
232 >              simError();
233 >            }
234 >            // We found an explicit Sutton-Chen interaction.  
235 >            // override all other metallic entries for this pair of atom types:
236 >            set<NonBondedInteraction*>::iterator it;
237 >            for (it = interactions_[key].begin();
238 >                 it != interactions_[key].end(); ++it) {
239 >              InteractionFamily ifam = (*it)->getFamily();
240 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
241 >            }
242 >            interactions_[key].insert(sc_);
243 >            metExplicit = true;
244            }
245 <          interactions_[key].insert(sc_);
246 <          metExplicit = true;
245 >          
246 >          if (nbiType->isMAW()) {
247 >            if (vdwExplicit) {
248 >              sprintf( painCave.errMsg,
249 >                       "InteractionManager::initialize found more than one "
250 >                       "explicit\n"
251 >                       "\tvan der Waals interaction for atom types %s - %s\n",
252 >                       atype1->getName().c_str(), atype2->getName().c_str());
253 >              painCave.severity = OPENMD_ERROR;
254 >              painCave.isFatal = 1;
255 >              simError();
256 >            }
257 >            // We found an explicit MAW interaction.  
258 >            // override all other vdw entries for this pair of atom types:
259 >            set<NonBondedInteraction*>::iterator it;
260 >            for (it = interactions_[key].begin();
261 >                 it != interactions_[key].end(); ++it) {
262 >              InteractionFamily ifam = (*it)->getFamily();
263 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
264 >            }
265 >            interactions_[key].insert(maw_);
266 >            vdwExplicit = true;
267 >          }        
268          }
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 –        }        
269        }
270      }
271      
272 <    // make sure every pair of atom types has a non-bonded interaction:
273 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
274 <         atype1 = atomTypes->nextType(i1)) {
275 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
276 <           atype2 = atomTypes->nextType(i2)) {
272 >    
273 >    // Make sure every pair of atom types in this simulation has a
274 >    // non-bonded interaction.  If not, just inform the user.
275 >
276 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
277 >    set<AtomType*>::iterator it, jt;
278 >
279 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
280 >      atype1 = (*it);
281 >      for (jt = it; jt != simTypes.end(); ++jt) {
282 >        atype2 = (*jt);
283          key = make_pair(atype1, atype2);
284          
285          if (interactions_[key].size() == 0) {
286            sprintf( painCave.errMsg,
287 <                   "InteractionManager unable to find an appropriate non-bonded\n"
288 <                   "\tinteraction for atom types %s - %s\n",
287 >                   "InteractionManager could not find a matching non-bonded\n"
288 >                   "\tinteraction for atom types %s - %s\n"
289 >                   "\tProceeding without this interaction.\n",
290                     atype1->getName().c_str(), atype2->getName().c_str());
291            painCave.severity = OPENMD_INFO;
292 <          painCave.isFatal = 1;
292 >          painCave.isFatal = 0;
293            simError();
294          }
295        }
296      }
297 <  }
298 <  
299 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
297 >
298 >    initialized_ = true;
299 >  }
300 >
301 >  void InteractionManager::setCutoffRadius(RealType rcut) {
302      
303 +    electrostatic_->setCutoffRadius(rcut);
304 +    eam_->setCutoffRadius(rcut);
305 +  }
306 +
307 +  void InteractionManager::doPrePair(InteractionData idat){
308 +    
309      if (!initialized_) initialize();
310 <          
311 <    DensityData ddat;
310 >        
311 >    // excluded interaction, so just return
312 >    if (idat.excluded) return;
313  
286 –    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;
291 –
292 –    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
314      set<NonBondedInteraction*>::iterator it;
315  
316 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
316 >    for (it = interactions_[ idat.atypes ].begin();
317 >         it != interactions_[ idat.atypes ].end(); ++it){
318        if ((*it)->getFamily() == METALLIC_FAMILY) {
319 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
319 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
320        }
321      }
322      
323      return;    
324    }
325    
326 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
326 >  void InteractionManager::doPreForce(SelfData sdat){
327  
328      if (!initialized_) initialize();
329 <          
330 <    FunctionalData fdat;
309 <
310 <    fdat.atype = typeMap_[*atid];
311 <    fdat.rho = *rho;
312 <    fdat.frho = *frho;
313 <    fdat.dfrhodrho = *dfrhodrho;
314 <
315 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
329 >    
330 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
331      set<NonBondedInteraction*>::iterator it;
332      
333      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
334        if ((*it)->getFamily() == METALLIC_FAMILY) {
335 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
335 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
336        }
337      }
338      
339      return;    
340    }
341  
342 <  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){
342 >  void InteractionManager::doPair(InteractionData idat){
343      
344      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;
345  
358 –    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
346      set<NonBondedInteraction*>::iterator it;
347  
348 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
349 <      (*it)->calcForce(idat);
363 <    
364 <    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();
348 >    for (it = interactions_[ idat.atypes ].begin();
349 >         it != interactions_[ idat.atypes ].end(); ++it) {
350  
351 <    return;    
352 <  }
351 >      // electrostatics still has to worry about indirect
352 >      // contributions from excluded pairs of atoms:
353  
354 <  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){
355 <
381 <    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);
400 <
401 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
402 <    set<NonBondedInteraction*>::iterator it;
403 <
404 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
405 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
406 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
354 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
355 >        (*it)->calcForce(idat);
356        }
357      }
358      
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();
421 –
359      return;    
360    }
361  
362 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
362 >  void InteractionManager::doSelfCorrection(SelfData sdat){
363  
364      if (!initialized_) initialize();
365      
366 <    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);
436 <
437 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
366 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
367      set<NonBondedInteraction*>::iterator it;
368  
369      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
370        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
371 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
371 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
372        }
373      }
374 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
449 <
374 >      
375      return;    
376    }
377  
453 –
378    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
379      if (!initialized_) initialize();
380 <    
380 >
381      AtomType* atype = typeMap_[*atid];
382  
383      pair<AtomType*, AtomType*> key = make_pair(atype, atype);
# Line 461 | Line 385 | namespace OpenMD {
385      RealType cutoff = 0.0;
386      
387      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
388 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
388 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
389      return cutoff;    
390    }
391  
# Line 473 | Line 397 | namespace OpenMD {
397      RealType cutoff = 0.0;
398      
399      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
400 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
400 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
401      return cutoff;    
402    }
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 –
403   } //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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