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

Comparing:
branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1550 by gezelter, Wed Apr 27 21:49:59 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 43 | Line 43 | namespace OpenMD {
43  
44   namespace OpenMD {
45  
46 <  InteractionManager* InteractionManager::_instance = NULL;
47 <  SimInfo* InteractionManager::info_ = NULL;
48 <  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_;
60 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
61 <
62 <  LJ* InteractionManager::lj_ = new LJ();
63 <  GB* InteractionManager::gb_ = new GB();
64 <  Sticky* InteractionManager::sticky_ = new Sticky();
65 <  Morse* InteractionManager::morse_ = new Morse();
66 <  EAM* InteractionManager::eam_ = new EAM();
67 <  SC* InteractionManager::sc_ = new SC();
68 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
69 <  MAW* InteractionManager::maw_ = new MAW();
70 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
71 <
72 <  InteractionManager* InteractionManager::Instance() {
73 <    if (!_instance) {
74 <      _instance = new InteractionManager();
75 <    }
76 <    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 86 | 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_);
91 –
92 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
93 –
94 –    // Force fields can set options on how to scale van der Waals and electrostatic
95 –    // interactions for atoms connected via bonds, bends and torsions
96 –    // in this case the topological distance between atoms is:
97 –    // 0 = topologically unconnected
98 –    // 1 = bonded together
99 –    // 2 = connected via a bend
100 –    // 3 = connected via a torsion
73  
102 –    vdwScale_[0] = 1.0;
103 –    vdwScale_[1] = fopts.getvdw12scale();
104 –    vdwScale_[2] = fopts.getvdw13scale();
105 –    vdwScale_[3] = fopts.getvdw14scale();
106 –
107 –    electrostaticScale_[0] = 1.0;
108 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
109 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
110 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
111 –
74      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76      AtomType* atype1;
# Line 280 | 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  
306 –    setupCutoffs();
307 –    setupSwitching();
308 –    setupNeighborlists();
309 –
310 –    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
311 –    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
312 –    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
313 –    //notifyFortranSkinThickness(&skinThickness_);
314 –
270      initialized_ = true;
271    }
317 –  
318 –  /**
319 –   * setupCutoffs
320 –   *
321 –   * Sets the values of cutoffRadius and cutoffMethod
322 –   *
323 –   * cutoffRadius : realType
324 –   *  If the cutoffRadius was explicitly set, use that value.
325 –   *  If the cutoffRadius was not explicitly set:
326 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
327 –   *      No electrostatic atoms?  Poll the atom types present in the
328 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
329 –   *      Use the maximum suggested value that was found.
330 –   *
331 –   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
332 –   *      If cutoffMethod was explicitly set, use that choice.
333 –   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
334 –   */
335 –  void InteractionManager::setupCutoffs() {
336 –    
337 –    Globals* simParams_ = info_->getSimParams();
338 –    
339 –    if (simParams_->haveCutoffRadius()) {
340 –      rCut_ = simParams_->getCutoffRadius();
341 –    } else {      
342 –      if (info_->usesElectrostaticAtoms()) {
343 –        sprintf(painCave.errMsg,
344 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
345 –                "\tOpenMD will use a default value of 12.0 angstroms"
346 –                "\tfor the cutoffRadius.\n");
347 –        painCave.isFatal = 0;
348 –        painCave.severity = OPENMD_INFO;
349 –        simError();
350 –        rCut_ = 12.0;
351 –      } else {
352 –        RealType thisCut;
353 –        set<AtomType*>::iterator i;
354 –        set<AtomType*> atomTypes;
355 –        atomTypes = info_->getSimulatedAtomTypes();        
356 –        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
357 –          thisCut = getSuggestedCutoffRadius((*i));
358 –          rCut_ = max(thisCut, rCut_);
359 –        }
360 –        sprintf(painCave.errMsg,
361 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
362 –                "\tOpenMD will use %lf angstroms.\n",
363 –                rCut_);
364 –        painCave.isFatal = 0;
365 –        painCave.severity = OPENMD_INFO;
366 –        simError();
367 –      }            
368 –    }
272  
273 <    map<string, CutoffMethod> stringToCutoffMethod;
371 <    stringToCutoffMethod["HARD"] = HARD;
372 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
373 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
374 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
375 <  
376 <    if (simParams_->haveCutoffMethod()) {
377 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
378 <      map<string, CutoffMethod>::iterator i;
379 <      i = stringToCutoffMethod.find(cutMeth);
380 <      if (i == stringToCutoffMethod.end()) {
381 <        sprintf(painCave.errMsg,
382 <                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
383 <                "\tShould be one of: "
384 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
385 <                cutMeth.c_str());
386 <        painCave.isFatal = 1;
387 <        painCave.severity = OPENMD_ERROR;
388 <        simError();
389 <      } else {
390 <        cutoffMethod_ = i->second;
391 <      }
392 <    } else {
393 <      sprintf(painCave.errMsg,
394 <              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
395 <              "\tOpenMD will use SHIFTED_FORCE.\n");
396 <        painCave.isFatal = 0;
397 <        painCave.severity = OPENMD_INFO;
398 <        simError();
399 <        cutoffMethod_ = SHIFTED_FORCE;        
400 <    }
401 <  }
402 <
403 <
404 <  /**
405 <   * setupSwitching
406 <   *
407 <   * Sets the values of switchingRadius and
408 <   *  If the switchingRadius was explicitly set, use that value (but check it)
409 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
410 <   */
411 <  void InteractionManager::setupSwitching() {
412 <    Globals* simParams_ = info_->getSimParams();
413 <
414 <    if (simParams_->haveSwitchingRadius()) {
415 <      rSwitch_ = simParams_->getSwitchingRadius();
416 <      if (rSwitch_ > rCut_) {        
417 <        sprintf(painCave.errMsg,
418 <                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
419 <                rSwitch_, rCut_);
420 <        painCave.isFatal = 1;
421 <        painCave.severity = OPENMD_ERROR;
422 <        simError();
423 <      }
424 <    } else {      
425 <      rSwitch_ = 0.85 * rCut_;
426 <      sprintf(painCave.errMsg,
427 <              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
428 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
429 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
430 <      painCave.isFatal = 0;
431 <      painCave.severity = OPENMD_WARNING;
432 <      simError();
433 <    }          
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274      
275 <    if (simParams_->haveSwitchingFunctionType()) {
276 <      string funcType = simParams_->getSwitchingFunctionType();
437 <      toUpper(funcType);
438 <      if (funcType == "CUBIC") {
439 <        sft_ = cubic;
440 <      } else {
441 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
442 <          sft_ = fifth_order_poly;
443 <        } else {
444 <          // throw error        
445 <          sprintf( painCave.errMsg,
446 <                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
447 <                   "\tswitchingFunctionType must be one of: "
448 <                   "\"cubic\" or \"fifth_order_polynomial\".",
449 <                   funcType.c_str() );
450 <          painCave.isFatal = 1;
451 <          painCave.severity = OPENMD_ERROR;
452 <          simError();
453 <        }          
454 <      }
455 <    }
456 <
457 <    switcher_->setSwitchType(sft_);
458 <    switcher_->setSwitch(rSwitch_, rCut_);
275 >    electrostatic_->setCutoffRadius(rcut);
276 >    eam_->setCutoffRadius(rcut);
277    }
278  
279 <  /**
280 <   * setupNeighborlists
463 <   *
464 <   *  If the skinThickness was explicitly set, use that value (but check it)
465 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
466 <   */
467 <  void InteractionManager::setupNeighborlists() {  
468 <
469 <    Globals* simParams_ = info_->getSimParams();    
470 <  
471 <    if (simParams_->haveSkinThickness()) {
472 <      skinThickness_ = simParams_->getSkinThickness();
473 <    } else {      
474 <      skinThickness_ = 1.0;
475 <      sprintf(painCave.errMsg,
476 <              "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n"
477 <              "\tOpenMD will use a default value of %f Angstroms\n"
478 <              "\tfor this simulation\n", skinThickness_);
479 <      painCave.severity = OPENMD_INFO;
480 <      painCave.isFatal = 0;
481 <      simError();
482 <    }            
483 <
484 <    listRadius_ = rCut_ + skinThickness_;
279 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
280 >    electrostatic_->setSwitchingRadius(rswitch);
281    }
282 <
487 <
282 >  
283    void InteractionManager::doPrePair(InteractionData idat){
284 <    
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 <    for (it = interactions_[idat.atypes].begin();
293 <         it != interactions_[idat.atypes].end(); ++it){
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        }
# Line 501 | Line 299 | namespace OpenMD {
299      return;    
300    }
301    
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 +    wrapData(idatThread, idat);
312 +
313 +    set<NonBondedInteraction*>::iterator it;
314 +
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(idat);
319 +      }
320 +    }
321 +
322 +    return;
323 +  }
324 +
325    void InteractionManager::doPreForce(SelfData sdat){
326  
327      if (!initialized_) initialize();
# Line 517 | Line 338 | namespace OpenMD {
338      return;    
339    }
340  
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 +                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 (kt = interactions_[ key ].begin();
356 +                                                kt != interactions_[ key ].end(); ++kt) {
357 +
358 +                                                (*kt)->initForce();
359 +                                }
360 +                        }
361 +                }
362 +
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::doPair(InteractionData idat){
374 <    
374 > //      printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
375      if (!initialized_) initialize();
376 <  
376 >
377      set<NonBondedInteraction*>::iterator it;
378  
379 <    for (it = interactions_[idat.atypes].begin();
380 <         it != interactions_[idat.atypes].end(); ++it)
381 <      (*it)->calcForce(idat);
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      return;    
391    }
392  
393 <  void InteractionManager::doSkipCorrection(InteractionData idat){
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 <    if (!initialized_) initialize();  
536 <    
427 >  void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
428      set<NonBondedInteraction*>::iterator it;
429 +    InteractionData idat;
430  
431 <    for (it = interactions_[idat.atypes].begin();
432 <         it != interactions_[idat.atypes].end(); ++it){
433 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
434 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
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;    
443 >
444 >    return;
445    }
446  
447    void InteractionManager::doSelfCorrection(SelfData sdat){

Diff Legend

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