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Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1868 by gezelter, Tue Apr 30 15:56:54 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      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
93      AtomType* atype1;
# Line 109 | Line 99 | namespace OpenMD {
99           atype1 = atomTypes->nextType(i1)) {
100        
101        // add it to the map:
112 –      AtomTypeProperties atp = atype1->getATP();    
102        
103        pair<map<int,AtomType*>::iterator,bool> ret;    
104 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
104 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
105        if (ret.second == false) {
106          sprintf( painCave.errMsg,
107                   "InteractionManager already had a previous entry with ident %d\n",
108 <                 atp.ident);
108 >                 atype1->getIdent());
109          painCave.severity = OPENMD_INFO;
110          painCave.isFatal = 0;
111          simError();                
# Line 134 | Line 123 | namespace OpenMD {
123          
124          bool vdwExplicit = false;
125          bool metExplicit = false;
126 <        bool hbExplicit = false;
126 >        // bool hbExplicit = false;
127                        
128          key = make_pair(atype1, atype2);
129          
# Line 167 | Line 156 | namespace OpenMD {
156          // look for an explicitly-set non-bonded interaction type using the
157          // two atom types.
158          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
159 +        
160 +        if (nbiType != NULL) {
161  
162 <        if (nbiType->isLennardJones()) {
163 <          // We found an explicit Lennard-Jones interaction.  
164 <          // override all other vdw entries for this pair of atom types:
165 <          set<NonBondedInteraction*>::iterator it;
166 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
167 <            InteractionFamily ifam = (*it)->getFamily();
168 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
162 >          if (nbiType->isLennardJones()) {
163 >            // We found an explicit Lennard-Jones interaction.  
164 >            // override all other vdw entries for this pair of atom types:
165 >            set<NonBondedInteraction*>::iterator it;
166 >            for (it = interactions_[key].begin();
167 >                 it != interactions_[key].end(); ++it) {
168 >              InteractionFamily ifam = (*it)->getFamily();
169 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
170 >            }
171 >            interactions_[key].insert(lj_);
172 >            vdwExplicit = true;
173            }
174 <          interactions_[key].insert(lj_);
175 <          vdwExplicit = true;
176 <        }
174 >          
175 >          if (nbiType->isMorse()) {
176 >            if (vdwExplicit) {
177 >              sprintf( painCave.errMsg,
178 >                       "InteractionManager::initialize found more than one "
179 >                       "explicit \n"
180 >                       "\tvan der Waals interaction for atom types %s - %s\n",
181 >                       atype1->getName().c_str(), atype2->getName().c_str());
182 >              painCave.severity = OPENMD_ERROR;
183 >              painCave.isFatal = 1;
184 >              simError();
185 >            }
186 >            // We found an explicit Morse interaction.  
187 >            // override all other vdw entries for this pair of atom types:
188 >            set<NonBondedInteraction*>::iterator it;
189 >            for (it = interactions_[key].begin();
190 >                 it != interactions_[key].end(); ++it) {
191 >              InteractionFamily ifam = (*it)->getFamily();
192 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
193 >            }
194 >            interactions_[key].insert(morse_);
195 >            vdwExplicit = true;
196 >          }
197  
198 <        if (nbiType->isMorse()) {
199 <          if (vdwExplicit) {
200 <            sprintf( painCave.errMsg,
201 <                     "InteractionManager::initialize found more than one explicit\n"
202 <                     "\tvan der Waals interaction for atom types %s - %s\n",
203 <                     atype1->getName().c_str(), atype2->getName().c_str());
204 <            painCave.severity = OPENMD_ERROR;
205 <            painCave.isFatal = 1;
206 <            simError();
198 >          if (nbiType->isRepulsivePower()) {
199 >            if (vdwExplicit) {
200 >              sprintf( painCave.errMsg,
201 >                       "InteractionManager::initialize found more than one "
202 >                       "explicit \n"
203 >                       "\tvan der Waals interaction for atom types %s - %s\n",
204 >                       atype1->getName().c_str(), atype2->getName().c_str());
205 >              painCave.severity = OPENMD_ERROR;
206 >              painCave.isFatal = 1;
207 >              simError();
208 >            }
209 >            // We found an explicit RepulsivePower interaction.  
210 >            // override all other vdw entries for this pair of atom types:
211 >            set<NonBondedInteraction*>::iterator it;
212 >            for (it = interactions_[key].begin();
213 >                 it != interactions_[key].end(); ++it) {
214 >              InteractionFamily ifam = (*it)->getFamily();
215 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
216 >            }
217 >            interactions_[key].insert(repulsivePower_);
218 >            vdwExplicit = true;
219            }
220 <          // We found an explicit Morse interaction.  
221 <          // override all other vdw entries for this pair of atom types:
222 <          set<NonBondedInteraction*>::iterator it;
223 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
224 <            InteractionFamily ifam = (*it)->getFamily();
225 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
220 >          
221 >          
222 >          if (nbiType->isEAM()) {
223 >            // We found an explicit EAM interaction.  
224 >            // override all other metallic entries for this pair of atom types:
225 >            set<NonBondedInteraction*>::iterator it;
226 >            for (it = interactions_[key].begin();
227 >                 it != interactions_[key].end(); ++it) {
228 >              InteractionFamily ifam = (*it)->getFamily();
229 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
230 >            }
231 >            interactions_[key].insert(eam_);
232 >            metExplicit = true;
233            }
234 <          interactions_[key].insert(morse_);
235 <          vdwExplicit = true;
236 <        }
237 <
238 <        if (nbiType->isEAM()) {
239 <          // We found an explicit EAM interaction.  
240 <          // override all other metallic entries for this pair of atom types:
241 <          set<NonBondedInteraction*>::iterator it;
242 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
243 <            InteractionFamily ifam = (*it)->getFamily();
244 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
234 >          
235 >          if (nbiType->isSC()) {
236 >            if (metExplicit) {
237 >              sprintf( painCave.errMsg,
238 >                       "InteractionManager::initialize found more than one "
239 >                       "explicit\n"
240 >                       "\tmetallic interaction for atom types %s - %s\n",
241 >                       atype1->getName().c_str(), atype2->getName().c_str());
242 >              painCave.severity = OPENMD_ERROR;
243 >              painCave.isFatal = 1;
244 >              simError();
245 >            }
246 >            // We found an explicit Sutton-Chen interaction.  
247 >            // override all other metallic entries for this pair of atom types:
248 >            set<NonBondedInteraction*>::iterator it;
249 >            for (it = interactions_[key].begin();
250 >                 it != interactions_[key].end(); ++it) {
251 >              InteractionFamily ifam = (*it)->getFamily();
252 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
253 >            }
254 >            interactions_[key].insert(sc_);
255 >            metExplicit = true;
256            }
257 <          interactions_[key].insert(eam_);
258 <          metExplicit = true;
257 >          
258 >          if (nbiType->isMAW()) {
259 >            if (vdwExplicit) {
260 >              sprintf( painCave.errMsg,
261 >                       "InteractionManager::initialize found more than one "
262 >                       "explicit\n"
263 >                       "\tvan der Waals interaction for atom types %s - %s\n",
264 >                       atype1->getName().c_str(), atype2->getName().c_str());
265 >              painCave.severity = OPENMD_ERROR;
266 >              painCave.isFatal = 1;
267 >              simError();
268 >            }
269 >            // We found an explicit MAW interaction.  
270 >            // override all other vdw entries for this pair of atom types:
271 >            set<NonBondedInteraction*>::iterator it;
272 >            for (it = interactions_[key].begin();
273 >                 it != interactions_[key].end(); ++it) {
274 >              InteractionFamily ifam = (*it)->getFamily();
275 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
276 >            }
277 >            interactions_[key].insert(maw_);
278 >            vdwExplicit = true;
279 >          }        
280          }
215 –
216 –        if (nbiType->isSC()) {
217 –          if (metExplicit) {
218 –            sprintf( painCave.errMsg,
219 –                     "InteractionManager::initialize found more than one explicit\n"
220 –                     "\tmetallic interaction for atom types %s - %s\n",
221 –                     atype1->getName().c_str(), atype2->getName().c_str());
222 –            painCave.severity = OPENMD_ERROR;
223 –            painCave.isFatal = 1;
224 –            simError();
225 –          }
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 –        }
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 –        }        
281        }
282      }
283      
284 <    // make sure every pair of atom types has a non-bonded interaction:
285 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
286 <         atype1 = atomTypes->nextType(i1)) {
287 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
288 <           atype2 = atomTypes->nextType(i2)) {
284 >    
285 >    // Make sure every pair of atom types in this simulation has a
286 >    // non-bonded interaction.  If not, just inform the user.
287 >
288 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
289 >    set<AtomType*>::iterator it, jt;
290 >
291 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
292 >      atype1 = (*it);
293 >      for (jt = it; jt != simTypes.end(); ++jt) {
294 >        atype2 = (*jt);
295          key = make_pair(atype1, atype2);
296          
297          if (interactions_[key].size() == 0) {
298            sprintf( painCave.errMsg,
299 <                   "InteractionManager unable to find an appropriate non-bonded\n"
300 <                   "\tinteraction for atom types %s - %s\n",
299 >                   "InteractionManager could not find a matching non-bonded\n"
300 >                   "\tinteraction for atom types %s - %s\n"
301 >                   "\tProceeding without this interaction.\n",
302                     atype1->getName().c_str(), atype2->getName().c_str());
303            painCave.severity = OPENMD_INFO;
304 <          painCave.isFatal = 1;
304 >          painCave.isFatal = 0;
305            simError();
306          }
307        }
308      }
309 <  }
310 <  
311 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
309 >
310 >    initialized_ = true;
311 >  }
312 >
313 >  void InteractionManager::setCutoffRadius(RealType rcut) {
314      
315 +    electrostatic_->setCutoffRadius(rcut);
316 +    eam_->setCutoffRadius(rcut);
317 +  }
318 +
319 +  void InteractionManager::doPrePair(InteractionData idat){
320 +    
321      if (!initialized_) initialize();
322 <          
323 <    DensityData ddat;
322 >        
323 >    // excluded interaction, so just return
324 >    if (idat.excluded) return;
325  
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);
326      set<NonBondedInteraction*>::iterator it;
327  
328 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
328 >    for (it = interactions_[ idat.atypes ].begin();
329 >         it != interactions_[ idat.atypes ].end(); ++it){
330        if ((*it)->getFamily() == METALLIC_FAMILY) {
331 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
331 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
332        }
333      }
334      
335      return;    
336    }
337    
338 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
338 >  void InteractionManager::doPreForce(SelfData sdat){
339  
340      if (!initialized_) initialize();
341 <          
342 <    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);
341 >    
342 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
343      set<NonBondedInteraction*>::iterator it;
344      
345      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
346        if ((*it)->getFamily() == METALLIC_FAMILY) {
347 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
347 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
348        }
349      }
350      
351      return;    
352    }
353  
354 <  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){
354 >  void InteractionManager::doPair(InteractionData idat){
355      
356      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;
357  
358 –    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
358      set<NonBondedInteraction*>::iterator it;
359  
360 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
361 <      (*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();
360 >    for (it = interactions_[ idat.atypes ].begin();
361 >         it != interactions_[ idat.atypes ].end(); ++it) {
362  
363 <    return;    
364 <  }
363 >      // electrostatics still has to worry about indirect
364 >      // contributions from excluded pairs of atoms:
365  
366 <  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){
367 <
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);
366 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
367 >        (*it)->calcForce(idat);
368        }
369      }
370      
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 –
371      return;    
372    }
373  
374 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
374 >  void InteractionManager::doSelfCorrection(SelfData sdat){
375  
376      if (!initialized_) initialize();
377      
378 <    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);
378 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
379      set<NonBondedInteraction*>::iterator it;
380  
381      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
382        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
383 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
383 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
384        }
385      }
386 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
449 <
386 >      
387      return;    
388    }
389  
453 –
390    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
391      if (!initialized_) initialize();
392 <    
392 >
393      AtomType* atype = typeMap_[*atid];
394  
395      pair<AtomType*, AtomType*> key = make_pair(atype, atype);
# Line 461 | 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    }
403  
# Line 473 | Line 409 | namespace OpenMD {
409      RealType cutoff = 0.0;
410      
411      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
412 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
412 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
413      return cutoff;    
414    }
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 –
415   } //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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