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root/OpenMD/branches/devel_omp/src/nonbonded/InteractionManager.cpp
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Comparing:
branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
branches/devel_omp/src/nonbonded/InteractionManager.cpp (file contents), Revision 1614 by mciznick, Tue Aug 23 20:55:51 2011 UTC

# Line 40 | Line 40
40   */
41  
42   #include "nonbonded/InteractionManager.hpp"
43 – #include "UseTheForce/doForces_interface.h"
43  
44   namespace OpenMD {
45  
46 <  InteractionManager* InteractionManager::_instance = NULL;
48 <  SimInfo* InteractionManager::info_ = NULL;
49 <  bool InteractionManager::initialized_ = false;
46 >  InteractionManager::InteractionManager() {
47  
48 <  RealType InteractionManager::rCut_ = 0.0;
49 <  RealType InteractionManager::rSwitch_ = 0.0;
50 <  RealType InteractionManager::skinThickness_ = 0.0;
51 <  RealType InteractionManager::listRadius_ = 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_;
61 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
62 <
63 <  LJ* InteractionManager::lj_ = new LJ();
64 <  GB* InteractionManager::gb_ = new GB();
65 <  Sticky* InteractionManager::sticky_ = new Sticky();
66 <  Morse* InteractionManager::morse_ = new Morse();
67 <  EAM* InteractionManager::eam_ = new EAM();
68 <  SC* InteractionManager::sc_ = new SC();
69 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
70 <  MAW* InteractionManager::maw_ = new MAW();
71 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
72 <
73 <  InteractionManager* InteractionManager::Instance() {
74 <    if (!_instance) {
75 <      _instance = new InteractionManager();
76 <    }
77 <    return _instance;
48 >    initialized_ = false;
49 >        
50 >    lj_ = new LJ();
51 >    gb_ = new GB();
52 >    sticky_ = new Sticky();
53 >    morse_ = new Morse();
54 >    eam_ = new EAM();
55 >    sc_ = new SC();
56 >    electrostatic_ = new Electrostatic();
57 >    maw_ = new MAW();
58    }
59  
60    void InteractionManager::initialize() {
# Line 87 | Line 67 | namespace OpenMD {
67      eam_->setForceField(forceField_);
68      sc_->setForceField(forceField_);
69      morse_->setForceField(forceField_);
70 +    electrostatic_->setSimInfo(info_);
71      electrostatic_->setForceField(forceField_);
72      maw_->setForceField(forceField_);
73  
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 = topologically unconnected
99 –    // 1 = bonded together
100 –    // 2 = connected via a bend
101 –    // 3 = connected via a torsion
102 –
103 –    vdwScale_[0] = 1.0;
104 –    vdwScale_[1] = fopts.getvdw12scale();
105 –    vdwScale_[2] = fopts.getvdw13scale();
106 –    vdwScale_[3] = fopts.getvdw14scale();
107 –
108 –    electrostaticScale_[0] = 1.0;
109 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
110 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112 –
74      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76      AtomType* atype1;
# Line 281 | Line 242 | namespace OpenMD {
242      }
243      
244      
245 <    // make sure every pair of atom types in this simulation has a
246 <    // non-bonded interaction:
245 >    // Make sure every pair of atom types in this simulation has a
246 >    // non-bonded interaction.  If not, just inform the user.
247  
248      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
249      set<AtomType*>::iterator it, jt;
250 +
251      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
252        atype1 = (*it);
253 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
253 >      for (jt = it; jt != simTypes.end(); ++jt) {
254          atype2 = (*jt);
255          key = make_pair(atype1, atype2);
256          
257          if (interactions_[key].size() == 0) {
258            sprintf( painCave.errMsg,
259 <                   "InteractionManager unable to find an appropriate non-bonded\n"
260 <                   "\tinteraction for atom types %s - %s\n",
259 >                   "InteractionManager could not find a matching non-bonded\n"
260 >                   "\tinteraction for atom types %s - %s\n"
261 >                   "\tProceeding without this interaction.\n",
262                     atype1->getName().c_str(), atype2->getName().c_str());
263            painCave.severity = OPENMD_INFO;
264 <          painCave.isFatal = 1;
264 >          painCave.isFatal = 0;
265            simError();
266          }
267        }
268      }
269  
270 <    setupCutoffs();
271 <    setupSwitching();
309 <    setupNeighborlists();
270 >    initialized_ = true;
271 >  }
272  
273 <    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
274 <    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
275 <    notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
276 <    notifyFortranSkinThickness(&skinThickness_);
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274 >    
275 >    electrostatic_->setCutoffRadius(rcut);
276 >    eam_->setCutoffRadius(rcut);
277 >  }
278  
279 <    initialized_ = true;
279 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
280 >    electrostatic_->setSwitchingRadius(rswitch);
281    }
282    
283 <  /**
284 <   * setupCutoffs
285 <   *
286 <   * Sets the values of cutoffRadius and cutoffMethod
287 <   *
288 <   * 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 <    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 <    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 <  }
283 >  void InteractionManager::doPrePair(InteractionData idat){
284 > //      printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
285 >    if (!initialized_) initialize();
286 >        
287 >    // excluded interaction, so just return
288 >    if (idat.excluded) return;
289  
290 +    set<NonBondedInteraction*>::iterator it;
291  
292 <  /**
293 <   * setupSwitching
294 <   *
295 <   * 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();
292 >    for (it = interactions_[ idat.atypes ].begin();
293 >         it != interactions_[ idat.atypes ].end(); ++it){
294 >      if ((*it)->getFamily() == METALLIC_FAMILY) {
295 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
296        }
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 –      }
297      }
298 <
299 <    switcher_->setSwitchType(sft_);
459 <    switcher_->setSwitch(rSwitch_, rCut_);
298 >    
299 >    return;    
300    }
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();    
301    
302 <    if (simParams_->haveSkinThickness()) {
303 <      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_;
302 >  void InteractionManager::initializeOMP() {
303 >        if (!initialized_) initialize();
304    }
305  
306 +  void InteractionManager::doPrePairOMP(InteractionDataPrv idatThread){
307 +        InteractionData idat;
308 +    // excluded interaction, so just return
309 +    if (idat.excluded) return;
310  
311 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
490 <    
491 <    if (!initialized_) initialize();
492 <          
493 <    DensityData ddat;
311 >    wrapData(idatThread, idat);
312  
495 –    ddat.atype1 = typeMap_[*atid1];
496 –    ddat.atype2 = typeMap_[*atid2];
497 –    ddat.rij = *rij;
498 –    ddat.rho_i_at_j = *rho_i_at_j;
499 –    ddat.rho_j_at_i = *rho_j_at_i;
500 –
501 –    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
313      set<NonBondedInteraction*>::iterator it;
314  
315 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
315 >    for (it = interactions_[ idat.atypes ].begin();
316 >         it != interactions_[ idat.atypes ].end(); ++it){
317        if ((*it)->getFamily() == METALLIC_FAMILY) {
318 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
318 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
319        }
320      }
321 <    
322 <    return;    
321 >
322 >    return;
323    }
512 –  
513 –  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
324  
325 <    if (!initialized_) initialize();
516 <          
517 <    FunctionalData fdat;
325 >  void InteractionManager::doPreForce(SelfData sdat){
326  
327 <    fdat.atype = typeMap_[*atid];
328 <    fdat.rho = *rho;
329 <    fdat.frho = *frho;
522 <    fdat.dfrhodrho = *dfrhodrho;
523 <
524 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
327 >    if (!initialized_) initialize();
328 >    
329 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
330      set<NonBondedInteraction*>::iterator it;
331      
332      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
333        if ((*it)->getFamily() == METALLIC_FAMILY) {
334 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
334 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
335        }
336      }
337      
338      return;    
339    }
340  
341 <  void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *sw, int *topoDist, RealType *A1, RealType *A2, RealType *eFrame1, RealType *eFrame2, RealType *vpair, RealType *pot, RealType  *f1, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){
342 <    
343 <    if (!initialized_) initialize();
344 <    
345 <    InteractionData idat;
346 <    
347 <    idat.atype1 = typeMap_[*atid1];
543 <    idat.atype2 = typeMap_[*atid2];
544 <    idat.d = Vector3d(d);
545 <    idat.rij = *r;
546 <    idat.r2 = *r2;
547 <    idat.sw = *sw;
548 <    idat.vdwMult = vdwScale_[*topoDist];
549 <    idat.electroMult = electrostaticScale_[*topoDist];
550 <    for (int i = 0; i < 4; i++) {
551 <      idat.vpair[i] = vpair[i];
552 <      idat.pot[i] = pot[i];
553 <    }
554 <    idat.f1 = Vector3d(f1[0], f1[1], f1[2]);
555 <    idat.eFrame1 = Mat3x3d(eFrame1);
556 <    idat.eFrame2 = Mat3x3d(eFrame2);
557 <    idat.A1 = RotMat3x3d(A1);
558 <    idat.A2 = RotMat3x3d(A2);
559 <    idat.t1 = Vector3d(t1);
560 <    idat.t2 = Vector3d(t2);
561 <    idat.rho1 = *rho1;
562 <    idat.rho2 = *rho2;
563 <    idat.dfrho1 = *dfrho1;
564 <    idat.dfrho2 = *dfrho2;
565 <    idat.fshift1 = *fshift1;
566 <    idat.fshift2 = *fshift2;
341 >  void InteractionManager::initNonbondedForces() {
342 >        pair<AtomType*, AtomType*> key;
343 >                set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
344 >                set<AtomType*>::iterator it, jt;
345 >                set<NonBondedInteraction*>::iterator kt;
346 >    AtomType* atype1;
347 >    AtomType* atype2;
348  
349 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
350 <    set<NonBondedInteraction*>::iterator it;
349 >                for (it = simTypes.begin(); it != simTypes.end(); ++it) {
350 >                        atype1 = (*it);
351 >                        for (jt = it; jt != simTypes.end(); ++jt) {
352 >                                atype2 = (*jt);
353 >                                key = make_pair(atype1, atype2);
354  
355 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
356 <      (*it)->calcForce(idat);
573 <    
574 <    for (int i = 0; i < 4; i++) {
575 <      vpair[i] = idat.vpair[i];
576 <      pot[i] = idat.pot[i];
577 <    }
355 >                                for (kt = interactions_[ key ].begin();
356 >                                                kt != interactions_[ key ].end(); ++kt) {
357  
358 <    for (int i = 0; i < 3; i++) {
359 <      f1[i] = idat.f1[i];
360 <      t1[i] = idat.t1[i];
361 <      t2[i] = idat.t2[i];
583 <    }
358 >                                                (*kt)->initForce();
359 >                                }
360 >                        }
361 >                }
362  
363 <    return;    
363 > /*      lj_->initForce();
364 >        electrostatic_->initForce();
365 >        sticky_->initForce();
366 >        eam_->initForce();
367 >        sc_->initForce();
368 >        gb_->initForce();*/
369 >
370 >                return;
371    }
372  
373 <  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){
374 <
373 >  void InteractionManager::doPair(InteractionData idat){
374 > //      printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
375      if (!initialized_) initialize();
591 –    
592 –    SkipCorrectionData skdat;
593 –    
594 –    skdat.atype1 = typeMap_[*atid1];
595 –    skdat.atype2 = typeMap_[*atid2];
596 –    skdat.d = Vector3d(d);
597 –    skdat.rij = *r;
598 –    skdat.skippedCharge1 = *skippedCharge1;
599 –    skdat.skippedCharge2 = *skippedCharge2;
600 –    skdat.sw = *sw;
601 –    skdat.electroMult = *electroMult;
602 –    for (int i = 0; i < 4; i++) {
603 –      skdat.vpair[i] = vpair[i];
604 –      skdat.pot[i] = pot[i];
605 –    }
606 –    skdat.f1 = Vector3d(f1);
607 –    skdat.eFrame1 = Mat3x3d(eFrame1);
608 –    skdat.eFrame2 = Mat3x3d(eFrame2);
609 –    skdat.t1 = Vector3d(t1);
610 –    skdat.t2 = Vector3d(t2);
376  
612 –    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
377      set<NonBondedInteraction*>::iterator it;
378  
379 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
380 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
381 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
379 >    for (it = interactions_[ idat.atypes ].begin();
380 >         it != interactions_[ idat.atypes ].end(); ++it) {
381 >
382 >      // electrostatics still has to worry about indirect
383 >      // contributions from excluded pairs of atoms:
384 >
385 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
386 >        (*it)->calcForce(idat);
387        }
388      }
389      
390 <    for (int i = 0; i < 4; i++) {
391 <      vpair[i] = skdat.vpair[i];
623 <      pot[i] = skdat.pot[i];
624 <    }
390 >    return;    
391 >  }
392  
393 <    for (int i = 0; i < 3; i++) {
394 <      f1[i] = skdat.f1[i];
395 <      t1[i] = skdat.t1[i];
396 <      t2[i] = skdat.t2[i];
393 >  void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) {
394 >        dst.A1 = src.A1;
395 >        dst.A2 = src.A2;
396 >        dst.atypes = src.atypes;
397 >        dst.d = &src.d;
398 >        dst.dfrho1 = src.dfrho1;
399 >        dst.dfrho2 = src.dfrho2;
400 >        dst.eFrame1 = src.eFrame1;
401 >        dst.eFrame2 = src.eFrame2;
402 >        dst.electroMult = &src.electroMult;
403 >        dst.excluded = src.excluded;
404 >        dst.f1 = &src.f1;
405 >        dst.frho1 = src.frho1;
406 >        dst.frho2 = src.frho2;
407 >        dst.particlePot1 = src.particlePot1;
408 >        dst.particlePot2 = src.particlePot2;
409 >        dst.pot = &src.pot;
410 >        dst.r2 = &src.r2;
411 >        dst.rcut = &src.rcut;
412 >        dst.rho1 = src.rho1;
413 >        dst.rho2 = src.rho2;
414 >        dst.rij = &src.rij;
415 >        dst.shiftedForce = src.shiftedForce;
416 >        dst.shiftedPot = src.shiftedPot;
417 >        dst.skippedCharge1 = src.skippedCharge1;
418 >        dst.skippedCharge2 = src.skippedCharge2;
419 >        dst.sw = &src.sw;
420 >        dst.t1 = src.t1;
421 >        dst.t2 = src.t2;
422 >        dst.topoDist = src.topoDist;
423 >        dst.vdwMult = &src.vdwMult;
424 >        dst.vpair = &src.vpair;
425 >  }
426 >
427 >  void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
428 >    set<NonBondedInteraction*>::iterator it;
429 >    InteractionData idat;
430 >
431 >    wrapData(idatThread, idat);
432 >
433 >    for (it = interactions_[ idat.atypes ].begin();
434 >         it != interactions_[ idat.atypes ].end(); ++it) {
435 >
436 >      // electrostatics still has to worry about indirect
437 >      // contributions from excluded pairs of atoms:
438 >
439 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
440 >        (*it)->calcForce(idat);
441 >      }
442      }
443  
444 <    return;    
444 >    return;
445    }
446  
447 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
447 >  void InteractionManager::doSelfCorrection(SelfData sdat){
448  
449      if (!initialized_) initialize();
450      
451 <    SelfCorrectionData scdat;
640 <    
641 <    scdat.atype = typeMap_[*atid];
642 <    scdat.eFrame = Mat3x3d(eFrame);
643 <    scdat.skippedCharge = *skippedCharge;
644 <    for (int i = 0; i < 4; i++){
645 <      scdat.pot[i] = pot[i];
646 <    }    
647 <    scdat.t = Vector3d(t);
648 <
649 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
451 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
452      set<NonBondedInteraction*>::iterator it;
453  
454      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
455        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
456 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
456 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
457        }
458      }
459        
658 –    t[0] = scdat.t.x();
659 –    t[1] = scdat.t.y();
660 –    t[2] = scdat.t.z();
661 –
460      return;    
461    }
462  
665 –
463    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
464      if (!initialized_) initialize();
465      
# Line 673 | Line 470 | namespace OpenMD {
470      RealType cutoff = 0.0;
471      
472      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
473 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
473 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
474      return cutoff;    
475    }
476  
# Line 685 | Line 482 | namespace OpenMD {
482      RealType cutoff = 0.0;
483      
484      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
485 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
485 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
486      return cutoff;    
487    }
691 –
692 –  void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
693 –                                     int *in_switching_region) {
694 –    bool isr = switcher_->getSwitch( *r2 , *sw, *dswdr, *r);    
695 –    *in_switching_region = (int)isr;
696 –  }
697 –
488   } //end namespace OpenMD
699 –
700 – extern "C" {
701 –  
702 – #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
703 – #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
704 – #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
705 – #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
706 – #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
707 – #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
708 – #define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH)
709 –
710 –  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
711 –                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
712 –            
713 –    return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij,
714 –                                                             rho_i_at_j,  
715 –                                                             rho_j_at_i);
716 –  }
717 –  void fortranDoPreForce(int *atid, RealType *rho, RealType *frho,
718 –                         RealType *dfrhodrho) {  
719 –    
720 –    return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho,
721 –                                                              dfrhodrho);    
722 –  }
723 –  
724 –  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2,
725 –                     RealType *sw, int *topoDist, RealType *A1, RealType *A2,
726 –                     RealType *eFrame1, RealType *eFrame2,
727 –                     RealType *vpair, RealType *pot,
728 –                     RealType *f1, RealType *t1, RealType *t2,
729 –                     RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2,
730 –                     RealType *fshift1, RealType *fshift2){
731 –    
732 –    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r, r2,
733 –                                                          sw, topoDist, A1, A2,
734 –                                                          eFrame1, eFrame2,
735 –                                                          vpair, pot,
736 –                                                          f1, t1, t2,
737 –                                                          rho1, rho2,
738 –                                                          dfrho1, dfrho2,
739 –                                                          fshift1, fshift2);
740 –  }
741 –  
742 –  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d,
743 –                               RealType *r, RealType *skippedCharge1,
744 –                               RealType *skippedCharge2, RealType *sw,
745 –                               RealType *electroMult, RealType *pot,
746 –                               RealType *vpair, RealType *f1,
747 –                               RealType *eFrame1, RealType *eFrame2,
748 –                               RealType *t1, RealType *t2){
749 –    
750 –    return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1,
751 –                                                                    atid2, d,
752 –                                                                    r,
753 –                                                                    skippedCharge1,
754 –                                                                    skippedCharge2,
755 –                                                                    sw, electroMult, pot,
756 –                                                                    vpair, f1, eFrame1,
757 –                                                                    eFrame2, t1, t2);
758 –  }
759 –  
760 –  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
761 –                               RealType *pot, RealType *t) {
762 –    
763 –    return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid,
764 –                                                                    eFrame,
765 –                                                                    skippedCharge,
766 –                                                                    pot, t);
767 –  }
768 –  RealType fortranGetCutoff(int *atid) {    
769 –    return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid);
770 –  }
771 –
772 –  void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
773 –                        int *in_switching_region) {    
774 –    return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r,
775 –                                                             in_switching_region);
776 –  }  
777 – }

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