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

Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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;
94      AtomType* atype2;
95      pair<AtomType*, AtomType*> key;
106 –    pair<set<NonBondedInteraction*>::iterator, bool> ret;
96      
97      for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
98           atype1 = atomTypes->nextType(i1)) {
99        
100        // add it to the map:
112 –      AtomTypeProperties atp = atype1->getATP();    
101        
102        pair<map<int,AtomType*>::iterator,bool> ret;    
103 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
103 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
104        if (ret.second == false) {
105          sprintf( painCave.errMsg,
106                   "InteractionManager already had a previous entry with ident %d\n",
107 <                 atp.ident);
107 >                 atype1->getIdent());
108          painCave.severity = OPENMD_INFO;
109          painCave.isFatal = 0;
110          simError();                
# Line 131 | Line 119 | namespace OpenMD {
119  
120        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
121          atype2 = (*it2).second;
122 <        
135 <        bool vdwExplicit = false;
136 <        bool metExplicit = false;
137 <        bool hbExplicit = false;
138 <                      
122 >                              
123          key = make_pair(atype1, atype2);
124          
125          if (atype1->isLennardJones() && atype2->isLennardJones()) {
# Line 167 | Line 151 | namespace OpenMD {
151          // look for an explicitly-set non-bonded interaction type using the
152          // two atom types.
153          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
154 +        
155 +        if (nbiType != NULL) {
156  
157 <        if (nbiType->isLennardJones()) {
158 <          // We found an explicit Lennard-Jones interaction.  
159 <          // override all other vdw entries for this pair of atom types:
174 <          set<NonBondedInteraction*>::iterator it;
175 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
176 <            InteractionFamily ifam = (*it)->getFamily();
177 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
178 <          }
179 <          interactions_[key].insert(lj_);
180 <          vdwExplicit = true;
181 <        }
157 >          bool vdwExplicit = false;
158 >          bool metExplicit = false;
159 >          // bool hbExplicit = false;
160  
161 <        if (nbiType->isMorse()) {
162 <          if (vdwExplicit) {
163 <            sprintf( painCave.errMsg,
164 <                     "InteractionManager::initialize found more than one explicit\n"
165 <                     "\tvan der Waals interaction for atom types %s - %s\n",
166 <                     atype1->getName().c_str(), atype2->getName().c_str());
167 <            painCave.severity = OPENMD_ERROR;
168 <            painCave.isFatal = 1;
169 <            simError();
161 >          if (nbiType->isLennardJones()) {
162 >            // We found an explicit Lennard-Jones interaction.  
163 >            // override all other vdw entries for this pair of atom types:
164 >            set<NonBondedInteraction*>::iterator it;
165 >            for (it = interactions_[key].begin();
166 >                 it != interactions_[key].end(); ++it) {
167 >              InteractionFamily ifam = (*it)->getFamily();
168 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
169 >            }
170 >            interactions_[key].insert(lj_);
171 >            vdwExplicit = true;
172            }
173 <          // We found an explicit Morse interaction.  
174 <          // override all other vdw entries for this pair of atom types:
175 <          set<NonBondedInteraction*>::iterator it;
176 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
177 <            InteractionFamily ifam = (*it)->getFamily();
178 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
179 <          }
180 <          interactions_[key].insert(morse_);
181 <          vdwExplicit = true;
182 <        }
183 <
184 <        if (nbiType->isEAM()) {
185 <          // We found an explicit EAM interaction.  
186 <          // override all other metallic entries for this pair of atom types:
187 <          set<NonBondedInteraction*>::iterator it;
188 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
189 <            InteractionFamily ifam = (*it)->getFamily();
190 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
191 <          }
192 <          interactions_[key].insert(eam_);
193 <          metExplicit = true;
194 <        }
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();
173 >          
174 >          if (nbiType->isMorse()) {
175 >            if (vdwExplicit) {
176 >              sprintf( painCave.errMsg,
177 >                       "InteractionManager::initialize found more than one "
178 >                       "explicit \n"
179 >                       "\tvan der Waals interaction for atom types %s - %s\n",
180 >                       atype1->getName().c_str(), atype2->getName().c_str());
181 >              painCave.severity = OPENMD_ERROR;
182 >              painCave.isFatal = 1;
183 >              simError();
184 >            }
185 >            // We found an explicit Morse interaction.  
186 >            // override all other vdw entries for this pair of atom types:
187 >            set<NonBondedInteraction*>::iterator it;
188 >            for (it = interactions_[key].begin();
189 >                 it != interactions_[key].end(); ++it) {
190 >              InteractionFamily ifam = (*it)->getFamily();
191 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
192 >            }
193 >            interactions_[key].insert(morse_);
194 >            vdwExplicit = true;
195            }
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 –        }
196  
197 <        if (nbiType->isMAW()) {
198 <          if (vdwExplicit) {
199 <            sprintf( painCave.errMsg,
200 <                     "InteractionManager::initialize found more than one explicit\n"
201 <                     "\tvan der Waals interaction for atom types %s - %s\n",
202 <                     atype1->getName().c_str(), atype2->getName().c_str());
203 <            painCave.severity = OPENMD_ERROR;
204 <            painCave.isFatal = 1;
205 <            simError();
197 >          if (nbiType->isRepulsivePower()) {
198 >            if (vdwExplicit) {
199 >              sprintf( painCave.errMsg,
200 >                       "InteractionManager::initialize found more than one "
201 >                       "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();
207 >            }
208 >            // We found an explicit RepulsivePower interaction.  
209 >            // override all other vdw entries for this pair of atom types:
210 >            set<NonBondedInteraction*>::iterator it;
211 >            for (it = interactions_[key].begin();
212 >                 it != interactions_[key].end(); ++it) {
213 >              InteractionFamily ifam = (*it)->getFamily();
214 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
215 >            }
216 >            interactions_[key].insert(repulsivePower_);
217 >            vdwExplicit = true;
218            }
219 <          // We found an explicit MAW interaction.  
220 <          // override all other vdw entries for this pair of atom types:
221 <          set<NonBondedInteraction*>::iterator it;
222 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
223 <            InteractionFamily ifam = (*it)->getFamily();
224 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
219 >          
220 >          
221 >          if (nbiType->isEAM()) {
222 >            // We found an explicit EAM interaction.  
223 >            // override all other metallic entries for this pair of atom types:
224 >            set<NonBondedInteraction*>::iterator it;
225 >            for (it = interactions_[key].begin();
226 >                 it != interactions_[key].end(); ++it) {
227 >              InteractionFamily ifam = (*it)->getFamily();
228 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
229 >            }
230 >            interactions_[key].insert(eam_);
231 >            metExplicit = true;
232            }
233 <          interactions_[key].insert(maw_);
234 <          vdwExplicit = true;
235 <        }        
233 >          
234 >          if (nbiType->isSC()) {
235 >            if (metExplicit) {
236 >              sprintf( painCave.errMsg,
237 >                       "InteractionManager::initialize found more than one "
238 >                       "explicit\n"
239 >                       "\tmetallic 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 Sutton-Chen interaction.  
246 >            // override all other metallic entries for this pair of atom types:
247 >            set<NonBondedInteraction*>::iterator it;
248 >            for (it = interactions_[key].begin();
249 >                 it != interactions_[key].end(); ++it) {
250 >              InteractionFamily ifam = (*it)->getFamily();
251 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
252 >            }
253 >            interactions_[key].insert(sc_);
254 >            metExplicit = true;
255 >          }
256 >          
257 >          if (nbiType->isMAW()) {
258 >            if (vdwExplicit) {
259 >              sprintf( painCave.errMsg,
260 >                       "InteractionManager::initialize found more than one "
261 >                       "explicit\n"
262 >                       "\tvan der Waals interaction for atom types %s - %s\n",
263 >                       atype1->getName().c_str(), atype2->getName().c_str());
264 >              painCave.severity = OPENMD_ERROR;
265 >              painCave.isFatal = 1;
266 >              simError();
267 >            }
268 >            // We found an explicit MAW interaction.  
269 >            // override all other vdw entries for this pair of atom types:
270 >            set<NonBondedInteraction*>::iterator it;
271 >            for (it = interactions_[key].begin();
272 >                 it != interactions_[key].end(); ++it) {
273 >              InteractionFamily ifam = (*it)->getFamily();
274 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
275 >            }
276 >            interactions_[key].insert(maw_);
277 >            vdwExplicit = true;
278 >          }        
279 >        }
280        }
281      }
282      
283 <    // make sure every pair of atom types has a non-bonded interaction:
284 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
285 <         atype1 = atomTypes->nextType(i1)) {
286 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
287 <           atype2 = atomTypes->nextType(i2)) {
283 >    
284 >    // Make sure every pair of atom types in this simulation has a
285 >    // non-bonded interaction.  If not, just inform the user.
286 >
287 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
288 >    set<AtomType*>::iterator it, jt;
289 >
290 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
291 >      atype1 = (*it);
292 >      for (jt = it; jt != simTypes.end(); ++jt) {
293 >        atype2 = (*jt);
294          key = make_pair(atype1, atype2);
295          
296          if (interactions_[key].size() == 0) {
297            sprintf( painCave.errMsg,
298 <                   "InteractionManager unable to find an appropriate non-bonded\n"
299 <                   "\tinteraction for atom types %s - %s\n",
298 >                   "InteractionManager could not find a matching non-bonded\n"
299 >                   "\tinteraction for atom types %s - %s\n"
300 >                   "\tProceeding without this interaction.\n",
301                     atype1->getName().c_str(), atype2->getName().c_str());
302            painCave.severity = OPENMD_INFO;
303 <          painCave.isFatal = 1;
303 >          painCave.isFatal = 0;
304            simError();
305          }
306        }
307      }
308 <  }
309 <  
310 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
308 >
309 >    initialized_ = true;
310 >  }
311 >
312 >  void InteractionManager::setCutoffRadius(RealType rcut) {
313      
314 +    electrostatic_->setCutoffRadius(rcut);
315 +    eam_->setCutoffRadius(rcut);
316 +  }
317 +
318 +  void InteractionManager::doPrePair(InteractionData idat){
319 +    
320      if (!initialized_) initialize();
321 <          
322 <    DensityData ddat;
321 >        
322 >    // excluded interaction, so just return
323 >    if (idat.excluded) return;
324  
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);
325      set<NonBondedInteraction*>::iterator it;
326  
327 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
327 >    for (it = interactions_[ idat.atypes ].begin();
328 >         it != interactions_[ idat.atypes ].end(); ++it){
329        if ((*it)->getFamily() == METALLIC_FAMILY) {
330 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
330 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
331        }
332      }
333      
334      return;    
335    }
336    
337 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
337 >  void InteractionManager::doPreForce(SelfData sdat){
338  
339      if (!initialized_) initialize();
340 <          
341 <    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);
340 >    
341 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
342      set<NonBondedInteraction*>::iterator it;
343      
344      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
345        if ((*it)->getFamily() == METALLIC_FAMILY) {
346 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
346 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
347        }
348      }
349      
350      return;    
351    }
352  
353 <  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){
353 >  void InteractionManager::doPair(InteractionData idat){
354      
355      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;
356  
358 –    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
357      set<NonBondedInteraction*>::iterator it;
358  
359 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
360 <      (*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();
359 >    for (it = interactions_[ idat.atypes ].begin();
360 >         it != interactions_[ idat.atypes ].end(); ++it) {
361  
362 <    return;    
363 <  }
362 >      // electrostatics still has to worry about indirect
363 >      // contributions from excluded pairs of atoms:
364  
365 <  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){
366 <
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);
365 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
366 >        (*it)->calcForce(idat);
367        }
368      }
369      
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 –
370      return;    
371    }
372  
373 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
373 >  void InteractionManager::doSelfCorrection(SelfData sdat){
374  
375      if (!initialized_) initialize();
376      
377 <    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);
377 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
378      set<NonBondedInteraction*>::iterator it;
379  
380      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
381        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
382 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
382 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
383        }
384      }
385 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
449 <
385 >      
386      return;    
387    }
388  
453 –
389    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
390      if (!initialized_) initialize();
391 <    
391 >
392      AtomType* atype = typeMap_[*atid];
393  
394      pair<AtomType*, AtomType*> key = make_pair(atype, atype);
# Line 461 | Line 396 | namespace OpenMD {
396      RealType cutoff = 0.0;
397      
398      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
399 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
399 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
400      return cutoff;    
401    }
402  
# Line 473 | Line 408 | namespace OpenMD {
408      RealType cutoff = 0.0;
409      
410      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
411 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
411 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
412      return cutoff;    
413    }
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 –
414   } //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 – }

Diff Legend

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