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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 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
branches/devel_omp/src/nonbonded/InteractionManager.cpp (file contents), Revision 1608 by mciznick, Tue Aug 9 01:58:56 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] = {0.0, 0.0, 0.0, 0.0};
55 <  RealType InteractionManager::electrostaticScale_[4] = {0.0, 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 = the atom itself
99 –    // 1 = bonded together
100 –    // 2 = connected via a bend
101 –    // 3 = connected via a torsion
102 –
103 –    vdwScale_[0] = 0.0;
104 –    vdwScale_[1] = fopts.getvdw12scale();
105 –    vdwScale_[2] = fopts.getvdw13scale();
106 –    vdwScale_[3] = fopts.getvdw14scale();
107 –
108 –    electrostaticScale_[0] = 0.0;
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  
307 –    setupCutoffs();
308 –    setupSwitching();
309 –    setupNeighborlists();
310 –    notifyFortranSkinThickness(&skinThickness_);
311 –
312 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
313 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
314 –    notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
315 –
316 –    int isError;
317 –    initFortranFF(&isError);
318 –
270      initialized_ = true;
271    }
272 <  
273 <  /**
323 <   * setupCutoffs
324 <   *
325 <   * Sets the values of cutoffRadius and cutoffMethod
326 <   *
327 <   * cutoffRadius : realType
328 <   *  If the cutoffRadius was explicitly set, use that value.
329 <   *  If the cutoffRadius was not explicitly set:
330 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
331 <   *      No electrostatic atoms?  Poll the atom types present in the
332 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
333 <   *      Use the maximum suggested value that was found.
334 <   *
335 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
336 <   *      If cutoffMethod was explicitly set, use that choice.
337 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
338 <   */
339 <  void InteractionManager::setupCutoffs() {
272 >
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274      
275 <    Globals* simParams_ = info_->getSimParams();
276 <    
277 <    if (simParams_->haveCutoffRadius()) {
344 <      rCut_ = simParams_->getCutoffRadius();
345 <    } else {      
346 <      if (info_->usesElectrostaticAtoms()) {
347 <        sprintf(painCave.errMsg,
348 <                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
349 <                "\tOpenMD will use a default value of 12.0 angstroms"
350 <                "\tfor the cutoffRadius.\n");
351 <        painCave.isFatal = 0;
352 <        painCave.severity = OPENMD_INFO;
353 <        simError();
354 <        rCut_ = 12.0;
355 <      } else {
356 <        RealType thisCut;
357 <        set<AtomType*>::iterator i;
358 <        set<AtomType*> atomTypes;
359 <        atomTypes = info_->getSimulatedAtomTypes();        
360 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
361 <          thisCut = getSuggestedCutoffRadius((*i));
362 <          rCut_ = max(thisCut, rCut_);
363 <        }
364 <        sprintf(painCave.errMsg,
365 <                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
366 <                "\tOpenMD will use %lf angstroms.\n",
367 <                rCut_);
368 <        painCave.isFatal = 0;
369 <        painCave.severity = OPENMD_INFO;
370 <        simError();
371 <      }            
372 <    }
275 >    electrostatic_->setCutoffRadius(rcut);
276 >    eam_->setCutoffRadius(rcut);
277 >  }
278  
279 <    map<string, CutoffMethod> stringToCutoffMethod;
280 <    stringToCutoffMethod["HARD"] = HARD;
376 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
377 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
378 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
379 <  
380 <    if (simParams_->haveCutoffMethod()) {
381 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
382 <      map<string, CutoffMethod>::iterator i;
383 <      i = stringToCutoffMethod.find(cutMeth);
384 <      if (i == stringToCutoffMethod.end()) {
385 <        sprintf(painCave.errMsg,
386 <                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
387 <                "\tShould be one of: "
388 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
389 <                cutMeth.c_str());
390 <        painCave.isFatal = 1;
391 <        painCave.severity = OPENMD_ERROR;
392 <        simError();
393 <      } else {
394 <        cutoffMethod_ = i->second;
395 <      }
396 <    } else {
397 <      sprintf(painCave.errMsg,
398 <              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
399 <              "\tOpenMD will use SHIFTED_FORCE.\n");
400 <        painCave.isFatal = 0;
401 <        painCave.severity = OPENMD_INFO;
402 <        simError();
403 <        cutoffMethod_ = SHIFTED_FORCE;        
404 <    }
279 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
280 >    electrostatic_->setSwitchingRadius(rswitch);
281    }
282 +  
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
412 <   *  If the switchingRadius was explicitly set, use that value (but check it)
413 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
414 <   */
415 <  void InteractionManager::setupSwitching() {
416 <    Globals* simParams_ = info_->getSimParams();
417 <
418 <    if (simParams_->haveSwitchingRadius()) {
419 <      rSwitch_ = simParams_->getSwitchingRadius();
420 <      if (rSwitch_ > rCut_) {        
421 <        sprintf(painCave.errMsg,
422 <                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
423 <                rSwitch_, rCut_);
424 <        painCave.isFatal = 1;
425 <        painCave.severity = OPENMD_ERROR;
426 <        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        }
297 <    } else {      
429 <      rSwitch_ = 0.85 * rCut_;
430 <      sprintf(painCave.errMsg,
431 <              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
432 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
433 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
434 <      painCave.isFatal = 0;
435 <      painCave.severity = OPENMD_WARNING;
436 <      simError();
437 <    }          
297 >    }*/
298      
299 <    if (simParams_->haveSwitchingFunctionType()) {
440 <      string funcType = simParams_->getSwitchingFunctionType();
441 <      toUpper(funcType);
442 <      if (funcType == "CUBIC") {
443 <        sft_ = cubic;
444 <      } else {
445 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
446 <          sft_ = fifth_order_poly;
447 <        } else {
448 <          // throw error        
449 <          sprintf( painCave.errMsg,
450 <                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
451 <                   "\tswitchingFunctionType must be one of: "
452 <                   "\"cubic\" or \"fifth_order_polynomial\".",
453 <                   funcType.c_str() );
454 <          painCave.isFatal = 1;
455 <          painCave.severity = OPENMD_ERROR;
456 <          simError();
457 <        }          
458 <      }
459 <    }
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_;
486 <
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){
491 <    
492 <    if (!initialized_) initialize();
493 <          
494 <    DensityData ddat;
311 >    wrapData(idatThread, idat);
312  
496 –    ddat.atype1 = typeMap_[*atid1];
497 –    ddat.atype2 = typeMap_[*atid2];
498 –    ddat.rij = *rij;
499 –    ddat.rho_i_at_j = *rho_i_at_j;
500 –    ddat.rho_j_at_i = *rho_j_at_i;
501 –
502 –    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    }
513 –  
514 –  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
324  
325 <    if (!initialized_) initialize();
517 <          
518 <    FunctionalData fdat;
325 >  void InteractionManager::doPreForce(SelfData sdat){
326  
327 <    fdat.atype = typeMap_[*atid];
328 <    fdat.rho = *rho;
329 <    fdat.frho = *frho;
523 <    fdat.dfrhodrho = *dfrhodrho;
524 <
525 <    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 *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){
342 <    
343 <    if (!initialized_) initialize();
540 <    
541 <    InteractionData idat;
542 <    
543 <    idat.atype1 = typeMap_[*atid1];
544 <    idat.atype2 = typeMap_[*atid2];
545 <    idat.d = Vector3d(d);
546 <    idat.rij = *r;
547 <    idat.r2 = *r2;
548 <    idat.rcut = *rcut;
549 <    idat.sw = *sw;
550 <    idat.vdwMult = vdwScale_[*topoDist];
551 <    idat.electroMult = electrostaticScale_[*topoDist];
552 <    idat.pot = *pot;
553 <    idat.vpair = *vpair;
554 <    idat.f1 = Vector3d(f1);
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::doPair(InteractionData idat){
342 >        printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
343 >    /*if (!initialized_) initialize();
344  
568 –    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
345      set<NonBondedInteraction*>::iterator it;
346  
347 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
348 <      (*it)->calcForce(idat);
573 <    
574 <    f1[0] = idat.f1.x();
575 <    f1[1] = idat.f1.y();
576 <    f1[2] = idat.f1.z();
577 <    
578 <    t1[0] = idat.t1.x();
579 <    t1[1] = idat.t1.y();
580 <    t1[2] = idat.t1.z();
581 <    
582 <    t2[0] = idat.t2.x();
583 <    t2[1] = idat.t2.y();
584 <    t2[2] = idat.t2.z();
347 >    for (it = interactions_[ idat.atypes ].begin();
348 >         it != interactions_[ idat.atypes ].end(); ++it) {
349  
350 +      // electrostatics still has to worry about indirect
351 +      // contributions from excluded pairs of atoms:
352 +
353 +      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
354 +        (*it)->calcForce(idat);
355 +      }
356 +    }*/
357 +    
358      return;    
359    }
360  
361 <  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){
361 >  void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) {
362 >        dst.A1 = src.A1;
363 >        dst.A2 = src.A2;
364 >        dst.atypes = src.atypes;
365 >        dst.d = &src.d;
366 >        dst.dfrho1 = src.dfrho1;
367 >        dst.dfrho2 = src.dfrho2;
368 >        dst.eFrame1 = src.eFrame1;
369 >        dst.eFrame2 = src.eFrame2;
370 >        dst.electroMult = &src.electroMult;
371 >        dst.excluded = src.excluded;
372 >        dst.f1 = &src.f1;
373 >        dst.frho1 = src.frho1;
374 >        dst.frho2 = src.frho2;
375 >        dst.particlePot1 = src.particlePot1;
376 >        dst.particlePot2 = src.particlePot2;
377 >        dst.pot = &src.pot;
378 >        dst.r2 = &src.r2;
379 >        dst.rcut = &src.rcut;
380 >        dst.rho1 = src.rho1;
381 >        dst.rho2 = src.rho2;
382 >        dst.rij = &src.rij;
383 >        dst.shiftedForce = src.shiftedForce;
384 >        dst.shiftedPot = src.shiftedPot;
385 >        dst.skippedCharge1 = src.skippedCharge1;
386 >        dst.skippedCharge2 = src.skippedCharge2;
387 >        dst.sw = &src.sw;
388 >        dst.t1 = src.t1;
389 >        dst.t2 = src.t2;
390 >        dst.topoDist = src.topoDist;
391 >        dst.vdwMult = &src.vdwMult;
392 >        dst.vpair = &src.vpair;
393 >  }
394  
395 <    if (!initialized_) initialize();
592 <    
593 <    SkipCorrectionData skdat;
594 <    
595 <    skdat.atype1 = typeMap_[*atid1];
596 <    skdat.atype2 = typeMap_[*atid2];
597 <    skdat.d = Vector3d(d);
598 <    skdat.rij = *r;
599 <    skdat.skippedCharge1 = *skippedCharge1;
600 <    skdat.skippedCharge2 = *skippedCharge2;
601 <    skdat.sw = *sw;
602 <    skdat.electroMult = *electroMult;
603 <    skdat.pot = *pot;
604 <    skdat.vpair = *vpair;
605 <    skdat.f1 = Vector3d(f1);
606 <    skdat.eFrame1 = Mat3x3d(eFrame1);
607 <    skdat.eFrame2 = Mat3x3d(eFrame2);
608 <    skdat.t1 = Vector3d(t1);
609 <    skdat.t2 = Vector3d(t2);
610 <
611 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
395 >  void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
396      set<NonBondedInteraction*>::iterator it;
397 +    InteractionData idat;
398  
399 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
400 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
401 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
399 >    wrapData(idatThread, idat);
400 >
401 >    for (it = interactions_[ idat.atypes ].begin();
402 >         it != interactions_[ idat.atypes ].end(); ++it) {
403 >
404 >      // electrostatics still has to worry about indirect
405 >      // contributions from excluded pairs of atoms:
406 >
407 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
408 >        (*it)->calcForce(idat);
409        }
410      }
619 –    
620 –    f1[0] = skdat.f1.x();
621 –    f1[1] = skdat.f1.y();
622 –    f1[2] = skdat.f1.z();
623 –    
624 –    t1[0] = skdat.t1.x();
625 –    t1[1] = skdat.t1.y();
626 –    t1[2] = skdat.t1.z();
627 –    
628 –    t2[0] = skdat.t2.x();
629 –    t2[1] = skdat.t2.y();
630 –    t2[2] = skdat.t2.z();
411  
412 <    return;    
412 >    return;
413    }
414  
415 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
415 >  void InteractionManager::doSelfCorrection(SelfData sdat){
416  
417      if (!initialized_) initialize();
418      
419 <    SelfCorrectionData scdat;
640 <    
641 <    scdat.atype = typeMap_[*atid];
642 <    scdat.eFrame = Mat3x3d(eFrame);
643 <    scdat.skippedCharge = *skippedCharge;
644 <    scdat.pot = *pot;
645 <    scdat.t = Vector3d(t);
646 <
647 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
419 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
420      set<NonBondedInteraction*>::iterator it;
421  
422      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
423        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
424 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
424 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
425        }
426      }
427 <        
656 <    t[0] = scdat.t.x();
657 <    t[1] = scdat.t.y();
658 <    t[2] = scdat.t.z();
659 <
427 >      
428      return;    
429    }
430  
663 –
431    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
432      if (!initialized_) initialize();
433      
# Line 671 | Line 438 | namespace OpenMD {
438      RealType cutoff = 0.0;
439      
440      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
441 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
441 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
442      return cutoff;    
443    }
444  
# Line 683 | Line 450 | namespace OpenMD {
450      RealType cutoff = 0.0;
451      
452      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
453 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
453 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
454      return cutoff;    
455    }
689 –
690 –
691 –  void InteractionManager::setSwitch(RealType *rIn, RealType *rOut) {
692 –    switcher_->setSwitch(*rIn, *rOut);    
693 –  }
694 –
695 –  void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
696 –                                     int *in_switching_region) {
697 –    bool isr = switcher_->getSwitch(*r2, *sw, *dswdr, *r);    
698 –    *in_switching_region = (int)isr;
699 –  }
700 –
456   } //end namespace OpenMD
702 –
703 – extern "C" {
704 –  
705 – #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
706 – #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
707 – #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
708 – #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
709 – #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
710 – #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
711 – #define fortranSetSwitch FC_FUNC(set_switch, SET_SWITCH)
712 – #define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH)
713 –
714 –  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
715 –                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
716 –            
717 –    return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij,
718 –                                                             rho_i_at_j,  
719 –                                                             rho_j_at_i);
720 –  }
721 –  void fortranDoPreForce(int *atid, RealType *rho, RealType *frho,
722 –                         RealType *dfrhodrho) {  
723 –    
724 –    return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho,
725 –                                                              dfrhodrho);    
726 –  }
727 –  
728 –  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r,
729 –                     RealType *r2, RealType *rcut, RealType *sw, int *topoDist,
730 –                     RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1,
731 –                     RealType *eFrame2, RealType *A1, RealType *A2,
732 –                     RealType *t1, RealType *t2, RealType *rho1, RealType *rho2,
733 –                     RealType *dfrho1, RealType *dfrho2, RealType *fshift1,
734 –                     RealType *fshift2){
735 –    
736 –    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r,
737 –                                                          r2, rcut, sw, topoDist,
738 –                                                          pot, vpair, f1,
739 –                                                          eFrame1, eFrame2,
740 –                                                          A1, A2, t1, t2, rho1,
741 –                                                          rho2, dfrho1, dfrho2,
742 –                                                          fshift1, fshift2);
743 –  }
744 –  
745 –  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d,
746 –                               RealType *r, RealType *skippedCharge1,
747 –                               RealType *skippedCharge2, RealType *sw,
748 –                               RealType *electroMult, RealType *pot,
749 –                               RealType *vpair, RealType *f1,
750 –                               RealType *eFrame1, RealType *eFrame2,
751 –                               RealType *t1, RealType *t2){
752 –    
753 –    return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1,
754 –                                                                    atid2, d,
755 –                                                                    r,
756 –                                                                    skippedCharge1,
757 –                                                                    skippedCharge2,
758 –                                                                    sw, electroMult, pot,
759 –                                                                    vpair, f1, eFrame1,
760 –                                                                    eFrame2, t1, t2);
761 –  }
762 –  
763 –  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
764 –                               RealType *pot, RealType *t) {
765 –    
766 –    return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid,
767 –                                                                    eFrame,
768 –                                                                    skippedCharge,
769 –                                                                    pot, t);
770 –  }
771 –  RealType fortranGetCutoff(int *atid) {    
772 –    return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid);
773 –  }
774 –
775 –  void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
776 –                        int *in_switching_region) {
777 –    
778 –    return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r,
779 –                                                             in_switching_region);
780 –  }
781 –
782 –  void fortranSetSwitch(RealType *rIn, RealType *rOut) {    
783 –    return OpenMD::InteractionManager::Instance()->setSwitch(rIn, rOut);
784 –  }
785 –  
786 – }

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