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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC

# Line 42 | Line 42 | namespace OpenMD {
42   #include "nonbonded/InteractionManager.hpp"
43  
44   namespace OpenMD {
45 <
45 >
46 >  InteractionManager* InteractionManager::_instance = NULL;
47 >  SimInfo* InteractionManager::info_ = NULL;
48    bool InteractionManager::initialized_ = false;
49 <  RealType InteractionManager::rCut_ = -1.0;
50 <  RealType InteractionManager::rSwitch_ = -1.0;
51 <  ForceField* InteractionManager::forceField_ = NULL;  
52 <  InteractionManager* InteractionManager::_instance = NULL;
49 >
50 >  RealType InteractionManager::rCut_ = 0.0;
51 >  RealType InteractionManager::rSwitch_ = 0.0;
52 >  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
53 >  SwitchingFunctionType InteractionManager::sft_ = cubic;
54 >  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
55 >  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
56 >
57    map<int, AtomType*> InteractionManager::typeMap_;
58    map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
59  
# Line 70 | Line 76 | namespace OpenMD {
76  
77    void InteractionManager::initialize() {
78      
79 +    ForceField* forceField_ = info_->getForceField();
80 +    
81      lj_->setForceField(forceField_);
82      gb_->setForceField(forceField_);
83      sticky_->setForceField(forceField_);
# Line 80 | Line 88 | namespace OpenMD {
88      maw_->setForceField(forceField_);
89  
90      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
91 +
92      // Force fields can set options on how to scale van der Waals and electrostatic
93      // interactions for atoms connected via bonds, bends and torsions
94      // in this case the topological distance between atoms is:
95 <    // 0 = the atom itself
95 >    // 0 = topologically unconnected
96      // 1 = bonded together
97      // 2 = connected via a bend
98      // 3 = connected via a torsion
99  
100 <    vdwScale_[0] = 0.0;
100 >    vdwScale_[0] = 1.0;
101      vdwScale_[1] = fopts.getvdw12scale();
102      vdwScale_[2] = fopts.getvdw13scale();
103      vdwScale_[3] = fopts.getvdw14scale();
104  
105 <    electrostaticScale_[0] = 0.0;
105 >    electrostaticScale_[0] = 1.0;
106      electrostaticScale_[1] = fopts.getelectrostatic12scale();
107      electrostaticScale_[2] = fopts.getelectrostatic13scale();
108 <    electrostaticScale_[3] = fopts.getelectrostatic14scale();
108 >    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
109  
110      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
111      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
# Line 167 | Line 176 | namespace OpenMD {
176          // look for an explicitly-set non-bonded interaction type using the
177          // two atom types.
178          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
179 +        
180 +        if (nbiType != NULL) {
181  
182 <        if (nbiType->isLennardJones()) {
183 <          // We found an explicit Lennard-Jones interaction.  
184 <          // override all other vdw entries for this pair of atom types:
185 <          set<NonBondedInteraction*>::iterator it;
186 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
187 <            InteractionFamily ifam = (*it)->getFamily();
188 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
182 >          if (nbiType->isLennardJones()) {
183 >            // We found an explicit Lennard-Jones interaction.  
184 >            // override all other vdw entries for this pair of atom types:
185 >            set<NonBondedInteraction*>::iterator it;
186 >            for (it = interactions_[key].begin();
187 >                 it != interactions_[key].end(); ++it) {
188 >              InteractionFamily ifam = (*it)->getFamily();
189 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
190 >            }
191 >            interactions_[key].insert(lj_);
192 >            vdwExplicit = true;
193            }
194 <          interactions_[key].insert(lj_);
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();
194 >          
195 >          if (nbiType->isMorse()) {
196 >            if (vdwExplicit) {
197 >              sprintf( painCave.errMsg,
198 >                       "InteractionManager::initialize found more than one "
199 >                       "explicit \n"
200 >                       "\tvan der Waals interaction for atom types %s - %s\n",
201 >                       atype1->getName().c_str(), atype2->getName().c_str());
202 >              painCave.severity = OPENMD_ERROR;
203 >              painCave.isFatal = 1;
204 >              simError();
205 >            }
206 >            // We found an explicit Morse interaction.  
207 >            // override all other vdw entries for this pair of atom types:
208 >            set<NonBondedInteraction*>::iterator it;
209 >            for (it = interactions_[key].begin();
210 >                 it != interactions_[key].end(); ++it) {
211 >              InteractionFamily ifam = (*it)->getFamily();
212 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
213 >            }
214 >            interactions_[key].insert(morse_);
215 >            vdwExplicit = true;
216            }
217 <          // We found an explicit Morse interaction.  
218 <          // override all other vdw entries for this pair of atom types:
219 <          set<NonBondedInteraction*>::iterator it;
220 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
221 <            InteractionFamily ifam = (*it)->getFamily();
222 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
217 >          
218 >          if (nbiType->isEAM()) {
219 >            // We found an explicit EAM interaction.  
220 >            // override all other metallic entries for this pair of atom types:
221 >            set<NonBondedInteraction*>::iterator it;
222 >            for (it = interactions_[key].begin();
223 >                 it != interactions_[key].end(); ++it) {
224 >              InteractionFamily ifam = (*it)->getFamily();
225 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
226 >            }
227 >            interactions_[key].insert(eam_);
228 >            metExplicit = true;
229            }
230 <          interactions_[key].insert(morse_);
231 <          vdwExplicit = true;
232 <        }
233 <
234 <        if (nbiType->isEAM()) {
235 <          // We found an explicit EAM interaction.  
236 <          // override all other metallic entries for this pair of atom types:
237 <          set<NonBondedInteraction*>::iterator it;
238 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
239 <            InteractionFamily ifam = (*it)->getFamily();
240 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
230 >          
231 >          if (nbiType->isSC()) {
232 >            if (metExplicit) {
233 >              sprintf( painCave.errMsg,
234 >                       "InteractionManager::initialize found more than one "
235 >                       "explicit\n"
236 >                       "\tmetallic interaction for atom types %s - %s\n",
237 >                       atype1->getName().c_str(), atype2->getName().c_str());
238 >              painCave.severity = OPENMD_ERROR;
239 >              painCave.isFatal = 1;
240 >              simError();
241 >            }
242 >            // We found an explicit Sutton-Chen interaction.  
243 >            // override all other metallic entries for this pair of atom types:
244 >            set<NonBondedInteraction*>::iterator it;
245 >            for (it = interactions_[key].begin();
246 >                 it != interactions_[key].end(); ++it) {
247 >              InteractionFamily ifam = (*it)->getFamily();
248 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
249 >            }
250 >            interactions_[key].insert(sc_);
251 >            metExplicit = true;
252            }
253 <          interactions_[key].insert(eam_);
254 <          metExplicit = true;
255 <        }
256 <
257 <        if (nbiType->isSC()) {
258 <          if (metExplicit) {
259 <            sprintf( painCave.errMsg,
260 <                     "InteractionManager::initialize found more than one explicit\n"
261 <                     "\tmetallic interaction for atom types %s - %s\n",
262 <                     atype1->getName().c_str(), atype2->getName().c_str());
263 <            painCave.severity = OPENMD_ERROR;
264 <            painCave.isFatal = 1;
265 <            simError();
266 <          }
267 <          // We found an explicit Sutton-Chen interaction.  
268 <          // override all other metallic entries for this pair of atom types:
269 <          set<NonBondedInteraction*>::iterator it;
270 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
271 <            InteractionFamily ifam = (*it)->getFamily();
272 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
273 <          }
274 <          interactions_[key].insert(sc_);
275 <          metExplicit = true;
253 >          
254 >          if (nbiType->isMAW()) {
255 >            if (vdwExplicit) {
256 >              sprintf( painCave.errMsg,
257 >                       "InteractionManager::initialize found more than one "
258 >                       "explicit\n"
259 >                       "\tvan der Waals interaction for atom types %s - %s\n",
260 >                       atype1->getName().c_str(), atype2->getName().c_str());
261 >              painCave.severity = OPENMD_ERROR;
262 >              painCave.isFatal = 1;
263 >              simError();
264 >            }
265 >            // We found an explicit MAW interaction.  
266 >            // override all other vdw entries for this pair of atom types:
267 >            set<NonBondedInteraction*>::iterator it;
268 >            for (it = interactions_[key].begin();
269 >                 it != interactions_[key].end(); ++it) {
270 >              InteractionFamily ifam = (*it)->getFamily();
271 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
272 >            }
273 >            interactions_[key].insert(maw_);
274 >            vdwExplicit = true;
275 >          }        
276          }
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 –        }        
277        }
278      }
279      
280 <    // make sure every pair of atom types has a non-bonded interaction:
281 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
282 <         atype1 = atomTypes->nextType(i1)) {
283 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
284 <           atype2 = atomTypes->nextType(i2)) {
280 >    
281 >    // make sure every pair of atom types in this simulation has a
282 >    // non-bonded interaction:
283 >
284 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
285 >    set<AtomType*>::iterator it, jt;
286 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
287 >      atype1 = (*it);
288 >      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
289 >        atype2 = (*jt);
290          key = make_pair(atype1, atype2);
291          
292          if (interactions_[key].size() == 0) {
# Line 275 | Line 300 | namespace OpenMD {
300          }
301        }
302      }
303 <  }
303 >
304 >    setupCutoffs();
305 >    setupSwitching();
306 >
307 >    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
308 >    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
309 >    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
310 >
311 >    initialized_ = true;
312 >  }
313    
314 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
314 >  /**
315 >   * setupCutoffs
316 >   *
317 >   * Sets the values of cutoffRadius and cutoffMethod
318 >   *
319 >   * cutoffRadius : realType
320 >   *  If the cutoffRadius was explicitly set, use that value.
321 >   *  If the cutoffRadius was not explicitly set:
322 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
323 >   *      No electrostatic atoms?  Poll the atom types present in the
324 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
325 >   *      Use the maximum suggested value that was found.
326 >   *
327 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
328 >   *      If cutoffMethod was explicitly set, use that choice.
329 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
330 >   */
331 >  void InteractionManager::setupCutoffs() {
332      
333 <    if (!initialized_) initialize();
334 <          
335 <    DensityData ddat;
333 >    Globals* simParams_ = info_->getSimParams();
334 >    
335 >    if (simParams_->haveCutoffRadius()) {
336 >      rCut_ = simParams_->getCutoffRadius();
337 >    } else {      
338 >      if (info_->usesElectrostaticAtoms()) {
339 >        sprintf(painCave.errMsg,
340 >                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
341 >                "\tOpenMD will use a default value of 12.0 angstroms"
342 >                "\tfor the cutoffRadius.\n");
343 >        painCave.isFatal = 0;
344 >        painCave.severity = OPENMD_INFO;
345 >        simError();
346 >        rCut_ = 12.0;
347 >      } else {
348 >        RealType thisCut;
349 >        set<AtomType*>::iterator i;
350 >        set<AtomType*> atomTypes;
351 >        atomTypes = info_->getSimulatedAtomTypes();        
352 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
353 >          thisCut = getSuggestedCutoffRadius((*i));
354 >          rCut_ = max(thisCut, rCut_);
355 >        }
356 >        sprintf(painCave.errMsg,
357 >                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
358 >                "\tOpenMD will use %lf angstroms.\n",
359 >                rCut_);
360 >        painCave.isFatal = 0;
361 >        painCave.severity = OPENMD_INFO;
362 >        simError();
363 >      }            
364 >    }
365  
366 <    ddat.atype1 = typeMap_[*atid1];
367 <    ddat.atype2 = typeMap_[*atid2];
368 <    ddat.rij = *rij;
369 <    ddat.rho_i_at_j = *rho_i_at_j;
370 <    ddat.rho_j_at_i = *rho_j_at_i;
366 >    map<string, CutoffMethod> stringToCutoffMethod;
367 >    stringToCutoffMethod["HARD"] = HARD;
368 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
369 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
370 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
371 >  
372 >    if (simParams_->haveCutoffMethod()) {
373 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
374 >      map<string, CutoffMethod>::iterator i;
375 >      i = stringToCutoffMethod.find(cutMeth);
376 >      if (i == stringToCutoffMethod.end()) {
377 >        sprintf(painCave.errMsg,
378 >                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
379 >                "\tShould be one of: "
380 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
381 >                cutMeth.c_str());
382 >        painCave.isFatal = 1;
383 >        painCave.severity = OPENMD_ERROR;
384 >        simError();
385 >      } else {
386 >        cutoffMethod_ = i->second;
387 >      }
388 >    } else {
389 >      sprintf(painCave.errMsg,
390 >              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
391 >              "\tOpenMD will use SHIFTED_FORCE.\n");
392 >        painCave.isFatal = 0;
393 >        painCave.severity = OPENMD_INFO;
394 >        simError();
395 >        cutoffMethod_ = SHIFTED_FORCE;        
396 >    }
397 >  }
398  
399 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
399 >
400 >  /**
401 >   * setupSwitching
402 >   *
403 >   * Sets the values of switchingRadius and
404 >   *  If the switchingRadius was explicitly set, use that value (but check it)
405 >   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
406 >   */
407 >  void InteractionManager::setupSwitching() {
408 >    Globals* simParams_ = info_->getSimParams();
409 >
410 >    if (simParams_->haveSwitchingRadius()) {
411 >      rSwitch_ = simParams_->getSwitchingRadius();
412 >      if (rSwitch_ > rCut_) {        
413 >        sprintf(painCave.errMsg,
414 >                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
415 >                rSwitch_, rCut_);
416 >        painCave.isFatal = 1;
417 >        painCave.severity = OPENMD_ERROR;
418 >        simError();
419 >      }
420 >    } else {      
421 >      rSwitch_ = 0.85 * rCut_;
422 >      sprintf(painCave.errMsg,
423 >              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
424 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
425 >              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
426 >      painCave.isFatal = 0;
427 >      painCave.severity = OPENMD_WARNING;
428 >      simError();
429 >    }          
430 >    
431 >    if (simParams_->haveSwitchingFunctionType()) {
432 >      string funcType = simParams_->getSwitchingFunctionType();
433 >      toUpper(funcType);
434 >      if (funcType == "CUBIC") {
435 >        sft_ = cubic;
436 >      } else {
437 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
438 >          sft_ = fifth_order_poly;
439 >        } else {
440 >          // throw error        
441 >          sprintf( painCave.errMsg,
442 >                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
443 >                   "\tswitchingFunctionType must be one of: "
444 >                   "\"cubic\" or \"fifth_order_polynomial\".",
445 >                   funcType.c_str() );
446 >          painCave.isFatal = 1;
447 >          painCave.severity = OPENMD_ERROR;
448 >          simError();
449 >        }          
450 >      }
451 >    }
452 >
453 >    switcher_->setSwitchType(sft_);
454 >    switcher_->setSwitch(rSwitch_, rCut_);
455 >  }
456 >
457 >  void InteractionManager::doPrePair(InteractionData idat){
458 >    
459 >    if (!initialized_) initialize();
460 >        
461      set<NonBondedInteraction*>::iterator it;
462  
463 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
463 >    for (it = interactions_[ *(idat.atypes) ].begin();
464 >         it != interactions_[ *(idat.atypes) ].end(); ++it){
465        if ((*it)->getFamily() == METALLIC_FAMILY) {
466 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
466 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
467        }
468      }
469      
470      return;    
471    }
472    
473 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
473 >  void InteractionManager::doPreForce(SelfData sdat){
474  
475      if (!initialized_) initialize();
476 <          
477 <    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);
476 >    
477 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
478      set<NonBondedInteraction*>::iterator it;
479      
480      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
481        if ((*it)->getFamily() == METALLIC_FAMILY) {
482 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
482 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
483        }
484      }
485      
486      return;    
487    }
488  
489 <  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){
489 >  void InteractionManager::doPair(InteractionData idat){
490      
491      if (!initialized_) initialize();
492 <    
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);
492 >  
493      set<NonBondedInteraction*>::iterator it;
494  
495 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
495 >    for (it = interactions_[ *(idat.atypes) ].begin();
496 >         it != interactions_[ *(idat.atypes) ].end(); ++it)
497        (*it)->calcForce(idat);
498      
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();
375 –
499      return;    
500    }
501  
502 <  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){
502 >  void InteractionManager::doSkipCorrection(InteractionData idat){
503  
504 <    if (!initialized_) initialize();
504 >    if (!initialized_) initialize();  
505      
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);
506      set<NonBondedInteraction*>::iterator it;
507  
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
508 >    for (it = interactions_[ *(idat.atypes) ].begin();
509 >         it != interactions_[ *(idat.atypes) ].end(); ++it){
510        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
511 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
511 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
512        }
513      }
514      
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 –
515      return;    
516    }
517  
518 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
518 >  void InteractionManager::doSelfCorrection(SelfData sdat){
519  
520      if (!initialized_) initialize();
521      
522 <    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);
522 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
523      set<NonBondedInteraction*>::iterator it;
524  
525      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
526        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
527 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
527 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
528        }
529      }
530 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
449 <
530 >      
531      return;    
532    }
533  
453 –
534    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
535      if (!initialized_) initialize();
536      
# Line 461 | Line 541 | namespace OpenMD {
541      RealType cutoff = 0.0;
542      
543      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
544 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
544 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
545      return cutoff;    
546    }
547  
# Line 473 | Line 553 | namespace OpenMD {
553      RealType cutoff = 0.0;
554      
555      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
556 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
556 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
557      return cutoff;    
558    }
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 –
559   } //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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