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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 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC

# Line 40 | Line 40
40   */
41  
42   #include "nonbonded/InteractionManager.hpp"
43 + #include "UseTheForce/doForces_interface.h"
44  
45   namespace OpenMD {
46 <
46 >
47 >  InteractionManager* InteractionManager::_instance = NULL;
48 >  SimInfo* InteractionManager::info_ = NULL;
49    bool InteractionManager::initialized_ = false;
50 <  RealType InteractionManager::rCut_ = -1.0;
51 <  RealType InteractionManager::rSwitch_ = -1.0;
52 <  ForceField* InteractionManager::forceField_ = NULL;  
53 <  InteractionManager* InteractionManager::_instance = NULL;
50 >
51 >  RealType InteractionManager::rCut_ = 0.0;
52 >  RealType InteractionManager::rSwitch_ = 0.0;
53 >  RealType InteractionManager::skinThickness_ = 0.0;
54 >  RealType InteractionManager::listRadius_ = 0.0;
55 >  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
56 >  SwitchingFunctionType InteractionManager::sft_ = cubic;
57 >  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
58 >  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
59 >
60    map<int, AtomType*> InteractionManager::typeMap_;
61    map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
62  
# Line 70 | Line 79 | namespace OpenMD {
79  
80    void InteractionManager::initialize() {
81      
82 +    ForceField* forceField_ = info_->getForceField();
83 +    
84      lj_->setForceField(forceField_);
85      gb_->setForceField(forceField_);
86      sticky_->setForceField(forceField_);
# Line 80 | Line 91 | namespace OpenMD {
91      maw_->setForceField(forceField_);
92  
93      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
94 +
95      // Force fields can set options on how to scale van der Waals and electrostatic
96      // interactions for atoms connected via bonds, bends and torsions
97      // in this case the topological distance between atoms is:
98 <    // 0 = the atom itself
98 >    // 0 = topologically unconnected
99      // 1 = bonded together
100      // 2 = connected via a bend
101      // 3 = connected via a torsion
102  
103 <    vdwScale_[0] = 0.0;
103 >    vdwScale_[0] = 1.0;
104      vdwScale_[1] = fopts.getvdw12scale();
105      vdwScale_[2] = fopts.getvdw13scale();
106      vdwScale_[3] = fopts.getvdw14scale();
107  
108 <    electrostaticScale_[0] = 0.0;
108 >    electrostaticScale_[0] = 1.0;
109      electrostaticScale_[1] = fopts.getelectrostatic12scale();
110      electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 <    electrostaticScale_[3] = fopts.getelectrostatic14scale();
111 >    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112  
113      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
114      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
# Line 167 | Line 179 | namespace OpenMD {
179          // look for an explicitly-set non-bonded interaction type using the
180          // two atom types.
181          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
182 +        
183 +        if (nbiType != NULL) {
184  
185 <        if (nbiType->isLennardJones()) {
186 <          // We found an explicit Lennard-Jones interaction.  
187 <          // override all other vdw entries for this pair of atom types:
188 <          set<NonBondedInteraction*>::iterator it;
189 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
190 <            InteractionFamily ifam = (*it)->getFamily();
191 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
185 >          if (nbiType->isLennardJones()) {
186 >            // We found an explicit Lennard-Jones 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(lj_);
195 >            vdwExplicit = true;
196            }
197 <          interactions_[key].insert(lj_);
198 <          vdwExplicit = true;
199 <        }
200 <
201 <        if (nbiType->isMorse()) {
202 <          if (vdwExplicit) {
203 <            sprintf( painCave.errMsg,
204 <                     "InteractionManager::initialize found more than one explicit\n"
205 <                     "\tvan der Waals interaction for atom types %s - %s\n",
206 <                     atype1->getName().c_str(), atype2->getName().c_str());
207 <            painCave.severity = OPENMD_ERROR;
208 <            painCave.isFatal = 1;
209 <            simError();
197 >          
198 >          if (nbiType->isMorse()) {
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 Morse 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(morse_);
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 >          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(morse_);
234 <          vdwExplicit = true;
235 <        }
236 <
237 <        if (nbiType->isEAM()) {
238 <          // We found an explicit EAM interaction.  
239 <          // override all other metallic entries for this pair of atom types:
240 <          set<NonBondedInteraction*>::iterator it;
241 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
242 <            InteractionFamily ifam = (*it)->getFamily();
243 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
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 <          interactions_[key].insert(eam_);
257 <          metExplicit = true;
258 <        }
259 <
260 <        if (nbiType->isSC()) {
261 <          if (metExplicit) {
262 <            sprintf( painCave.errMsg,
263 <                     "InteractionManager::initialize found more than one explicit\n"
264 <                     "\tmetallic interaction for atom types %s - %s\n",
265 <                     atype1->getName().c_str(), atype2->getName().c_str());
266 <            painCave.severity = OPENMD_ERROR;
267 <            painCave.isFatal = 1;
268 <            simError();
269 <          }
270 <          // We found an explicit Sutton-Chen interaction.  
271 <          // override all other metallic entries for this pair of atom types:
272 <          set<NonBondedInteraction*>::iterator it;
273 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
274 <            InteractionFamily ifam = (*it)->getFamily();
275 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
276 <          }
277 <          interactions_[key].insert(sc_);
278 <          metExplicit = true;
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          }
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 –        }        
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:
286 >
287 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
288 >    set<AtomType*>::iterator it, jt;
289 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
290 >      atype1 = (*it);
291 >      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
292 >        atype2 = (*jt);
293          key = make_pair(atype1, atype2);
294          
295          if (interactions_[key].size() == 0) {
# Line 275 | Line 303 | namespace OpenMD {
303          }
304        }
305      }
306 <  }
306 >
307 >    setupCutoffs();
308 >    setupSwitching();
309 >    setupNeighborlists();
310 >
311 >    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
312 >    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
313 >    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
314 >    //notifyFortranSkinThickness(&skinThickness_);
315 >
316 >    initialized_ = true;
317 >  }
318    
319 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
319 >  /**
320 >   * setupCutoffs
321 >   *
322 >   * Sets the values of cutoffRadius and cutoffMethod
323 >   *
324 >   * cutoffRadius : realType
325 >   *  If the cutoffRadius was explicitly set, use that value.
326 >   *  If the cutoffRadius was not explicitly set:
327 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
328 >   *      No electrostatic atoms?  Poll the atom types present in the
329 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
330 >   *      Use the maximum suggested value that was found.
331 >   *
332 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
333 >   *      If cutoffMethod was explicitly set, use that choice.
334 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
335 >   */
336 >  void InteractionManager::setupCutoffs() {
337      
338 <    if (!initialized_) initialize();
339 <          
340 <    DensityData ddat;
338 >    Globals* simParams_ = info_->getSimParams();
339 >    
340 >    if (simParams_->haveCutoffRadius()) {
341 >      rCut_ = simParams_->getCutoffRadius();
342 >    } else {      
343 >      if (info_->usesElectrostaticAtoms()) {
344 >        sprintf(painCave.errMsg,
345 >                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
346 >                "\tOpenMD will use a default value of 12.0 angstroms"
347 >                "\tfor the cutoffRadius.\n");
348 >        painCave.isFatal = 0;
349 >        painCave.severity = OPENMD_INFO;
350 >        simError();
351 >        rCut_ = 12.0;
352 >      } else {
353 >        RealType thisCut;
354 >        set<AtomType*>::iterator i;
355 >        set<AtomType*> atomTypes;
356 >        atomTypes = info_->getSimulatedAtomTypes();        
357 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
358 >          thisCut = getSuggestedCutoffRadius((*i));
359 >          rCut_ = max(thisCut, rCut_);
360 >        }
361 >        sprintf(painCave.errMsg,
362 >                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
363 >                "\tOpenMD will use %lf angstroms.\n",
364 >                rCut_);
365 >        painCave.isFatal = 0;
366 >        painCave.severity = OPENMD_INFO;
367 >        simError();
368 >      }            
369 >    }
370  
371 <    ddat.atype1 = typeMap_[*atid1];
372 <    ddat.atype2 = typeMap_[*atid2];
373 <    ddat.rij = *rij;
374 <    ddat.rho_i_at_j = *rho_i_at_j;
375 <    ddat.rho_j_at_i = *rho_j_at_i;
371 >    map<string, CutoffMethod> stringToCutoffMethod;
372 >    stringToCutoffMethod["HARD"] = HARD;
373 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
374 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
375 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
376 >  
377 >    if (simParams_->haveCutoffMethod()) {
378 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
379 >      map<string, CutoffMethod>::iterator i;
380 >      i = stringToCutoffMethod.find(cutMeth);
381 >      if (i == stringToCutoffMethod.end()) {
382 >        sprintf(painCave.errMsg,
383 >                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
384 >                "\tShould be one of: "
385 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
386 >                cutMeth.c_str());
387 >        painCave.isFatal = 1;
388 >        painCave.severity = OPENMD_ERROR;
389 >        simError();
390 >      } else {
391 >        cutoffMethod_ = i->second;
392 >      }
393 >    } else {
394 >      sprintf(painCave.errMsg,
395 >              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
396 >              "\tOpenMD will use SHIFTED_FORCE.\n");
397 >        painCave.isFatal = 0;
398 >        painCave.severity = OPENMD_INFO;
399 >        simError();
400 >        cutoffMethod_ = SHIFTED_FORCE;        
401 >    }
402 >  }
403  
404 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
404 >
405 >  /**
406 >   * setupSwitching
407 >   *
408 >   * Sets the values of switchingRadius and
409 >   *  If the switchingRadius was explicitly set, use that value (but check it)
410 >   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
411 >   */
412 >  void InteractionManager::setupSwitching() {
413 >    Globals* simParams_ = info_->getSimParams();
414 >
415 >    if (simParams_->haveSwitchingRadius()) {
416 >      rSwitch_ = simParams_->getSwitchingRadius();
417 >      if (rSwitch_ > rCut_) {        
418 >        sprintf(painCave.errMsg,
419 >                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
420 >                rSwitch_, rCut_);
421 >        painCave.isFatal = 1;
422 >        painCave.severity = OPENMD_ERROR;
423 >        simError();
424 >      }
425 >    } else {      
426 >      rSwitch_ = 0.85 * rCut_;
427 >      sprintf(painCave.errMsg,
428 >              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
429 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
430 >              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
431 >      painCave.isFatal = 0;
432 >      painCave.severity = OPENMD_WARNING;
433 >      simError();
434 >    }          
435 >    
436 >    if (simParams_->haveSwitchingFunctionType()) {
437 >      string funcType = simParams_->getSwitchingFunctionType();
438 >      toUpper(funcType);
439 >      if (funcType == "CUBIC") {
440 >        sft_ = cubic;
441 >      } else {
442 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
443 >          sft_ = fifth_order_poly;
444 >        } else {
445 >          // throw error        
446 >          sprintf( painCave.errMsg,
447 >                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
448 >                   "\tswitchingFunctionType must be one of: "
449 >                   "\"cubic\" or \"fifth_order_polynomial\".",
450 >                   funcType.c_str() );
451 >          painCave.isFatal = 1;
452 >          painCave.severity = OPENMD_ERROR;
453 >          simError();
454 >        }          
455 >      }
456 >    }
457 >
458 >    switcher_->setSwitchType(sft_);
459 >    switcher_->setSwitch(rSwitch_, rCut_);
460 >  }
461 >
462 >  /**
463 >   * setupNeighborlists
464 >   *
465 >   *  If the skinThickness was explicitly set, use that value (but check it)
466 >   *  If the skinThickness was not explicitly set: use 1.0 angstroms
467 >   */
468 >  void InteractionManager::setupNeighborlists() {  
469 >
470 >    Globals* simParams_ = info_->getSimParams();    
471 >  
472 >    if (simParams_->haveSkinThickness()) {
473 >      skinThickness_ = simParams_->getSkinThickness();
474 >    } else {      
475 >      skinThickness_ = 1.0;
476 >      sprintf(painCave.errMsg,
477 >              "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n"
478 >              "\tOpenMD will use a default value of %f Angstroms\n"
479 >              "\tfor this simulation\n", skinThickness_);
480 >      painCave.severity = OPENMD_INFO;
481 >      painCave.isFatal = 0;
482 >      simError();
483 >    }            
484 >
485 >    listRadius_ = rCut_ + skinThickness_;
486 >  }
487 >
488 >
489 >  void InteractionManager::doPrePair(InteractionData idat){
490 >    
491 >    if (!initialized_) initialize();
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        if ((*it)->getFamily() == METALLIC_FAMILY) {
498 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
498 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
499        }
500      }
501      
502      return;    
503    }
504    
505 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
505 >  void InteractionManager::doPreForce(SelfData sdat){
506  
507      if (!initialized_) initialize();
508 <          
509 <    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);
508 >    
509 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
510      set<NonBondedInteraction*>::iterator it;
511      
512      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
513        if ((*it)->getFamily() == METALLIC_FAMILY) {
514 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
514 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
515        }
516      }
517      
518      return;    
519    }
520  
521 <  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){
521 >  void InteractionManager::doPair(InteractionData idat){
522      
523      if (!initialized_) initialize();
524 <    
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);
524 >  
525      set<NonBondedInteraction*>::iterator it;
526  
527 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
527 >    for (it = interactions_[idat.atypes].begin();
528 >         it != interactions_[idat.atypes].end(); ++it)
529        (*it)->calcForce(idat);
530      
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 –
531      return;    
532    }
533  
534 <  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){
534 >  void InteractionManager::doSkipCorrection(InteractionData idat){
535  
536 <    if (!initialized_) initialize();
536 >    if (!initialized_) initialize();  
537      
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);
538      set<NonBondedInteraction*>::iterator it;
539  
540 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
540 >    for (it = interactions_[idat.atypes].begin();
541 >         it != interactions_[idat.atypes].end(); ++it){
542        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
543 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
543 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
544        }
545      }
546      
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 –
547      return;    
548    }
549  
550 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
550 >  void InteractionManager::doSelfCorrection(SelfData sdat){
551  
552      if (!initialized_) initialize();
553      
554 <    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);
554 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
555      set<NonBondedInteraction*>::iterator it;
556  
557      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
558        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
559 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
559 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
560        }
561      }
562 <        
446 <    t[0] = scdat.t.x();
447 <    t[1] = scdat.t.y();
448 <    t[2] = scdat.t.z();
449 <
562 >      
563      return;    
564    }
565  
453 –
566    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
567      if (!initialized_) initialize();
568      
# Line 461 | Line 573 | namespace OpenMD {
573      RealType cutoff = 0.0;
574      
575      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
576 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
576 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
577      return cutoff;    
578    }
579  
# Line 473 | Line 585 | namespace OpenMD {
585      RealType cutoff = 0.0;
586      
587      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
588 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
588 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
589      return cutoff;    
590    }
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 –
591   } //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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