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Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "nonbonded/InteractionManager.hpp"
44  
45   namespace OpenMD {
46  
47 <  InteractionManager* InteractionManager::_instance = NULL;
47 <  SimInfo* InteractionManager::info_ = NULL;
48 <  bool InteractionManager::initialized_ = false;
47 >  InteractionManager::InteractionManager() {
48  
49 <  RealType InteractionManager::rCut_ = 0.0;
50 <  RealType InteractionManager::rSwitch_ = 0.0;
51 <  RealType InteractionManager::skinThickness_ = 0.0;
52 <  RealType InteractionManager::listRadius_ = 0.0;
53 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
54 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
55 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
56 <  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
49 >    initialized_ = false;
50 >        
51 >    lj_ = new LJ();
52 >    gb_ = new GB();
53 >    sticky_ = new Sticky();
54 >    morse_ = new Morse();
55 >    repulsivePower_ = new RepulsivePower();
56 >    eam_ = new EAM();
57 >    sc_ = new SC();
58 >    electrostatic_ = new Electrostatic();
59 >    maw_ = new MAW();
60 >  }
61  
62 <  map<int, AtomType*> InteractionManager::typeMap_;
63 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
64 <
65 <  LJ* InteractionManager::lj_ = new LJ();
66 <  GB* InteractionManager::gb_ = new GB();
67 <  Sticky* InteractionManager::sticky_ = new Sticky();
68 <  Morse* InteractionManager::morse_ = new Morse();
69 <  EAM* InteractionManager::eam_ = new EAM();
70 <  SC* InteractionManager::sc_ = new SC();
71 <  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;
62 >  InteractionManager::~InteractionManager() {
63 >    delete lj_;
64 >    delete gb_;
65 >    delete sticky_;
66 >    delete morse_;
67 >    delete repulsivePower_;
68 >    delete eam_;
69 >    delete sc_;
70 >    delete electrostatic_;
71 >    delete maw_;
72    }
73  
74    void InteractionManager::initialize() {
75 <    
75 >
76 >    if (initialized_) return;
77 >
78      ForceField* forceField_ = info_->getForceField();
79      
80      lj_->setForceField(forceField_);
# Line 86 | Line 83 | namespace OpenMD {
83      eam_->setForceField(forceField_);
84      sc_->setForceField(forceField_);
85      morse_->setForceField(forceField_);
86 +    electrostatic_->setSimInfo(info_);
87      electrostatic_->setForceField(forceField_);
88      maw_->setForceField(forceField_);
89 +    repulsivePower_->setForceField(forceField_);
90  
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
101 –
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 –
91      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
93      AtomType* atype1;
94      AtomType* atype2;
95      pair<AtomType*, AtomType*> key;
117 –    pair<set<NonBondedInteraction*>::iterator, bool> ret;
96      
97      for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
98           atype1 = atomTypes->nextType(i1)) {
99        
100        // add it to the map:
123 –      AtomTypeProperties atp = atype1->getATP();    
101        
102        pair<map<int,AtomType*>::iterator,bool> ret;    
103 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
103 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
104        if (ret.second == false) {
105          sprintf( painCave.errMsg,
106                   "InteractionManager already had a previous entry with ident %d\n",
107 <                 atp.ident);
107 >                 atype1->getIdent());
108          painCave.severity = OPENMD_INFO;
109          painCave.isFatal = 0;
110          simError();                
# Line 142 | Line 119 | namespace OpenMD {
119  
120        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
121          atype2 = (*it2).second;
122 <        
146 <        bool vdwExplicit = false;
147 <        bool metExplicit = false;
148 <        bool hbExplicit = false;
149 <                      
122 >                              
123          key = make_pair(atype1, atype2);
124          
125          if (atype1->isLennardJones() && atype2->isLennardJones()) {
# Line 181 | Line 154 | namespace OpenMD {
154          
155          if (nbiType != NULL) {
156  
157 +          bool vdwExplicit = false;
158 +          bool metExplicit = false;
159 +          // bool hbExplicit = false;
160 +
161            if (nbiType->isLennardJones()) {
162              // We found an explicit Lennard-Jones interaction.  
163              // override all other vdw entries for this pair of atom types:
# Line 216 | Line 193 | namespace OpenMD {
193              interactions_[key].insert(morse_);
194              vdwExplicit = true;
195            }
196 +
197 +          if (nbiType->isRepulsivePower()) {
198 +            if (vdwExplicit) {
199 +              sprintf( painCave.errMsg,
200 +                       "InteractionManager::initialize found more than one "
201 +                       "explicit \n"
202 +                       "\tvan der Waals interaction for atom types %s - %s\n",
203 +                       atype1->getName().c_str(), atype2->getName().c_str());
204 +              painCave.severity = OPENMD_ERROR;
205 +              painCave.isFatal = 1;
206 +              simError();
207 +            }
208 +            // We found an explicit RepulsivePower interaction.  
209 +            // override all other vdw entries for this pair of atom types:
210 +            set<NonBondedInteraction*>::iterator it;
211 +            for (it = interactions_[key].begin();
212 +                 it != interactions_[key].end(); ++it) {
213 +              InteractionFamily ifam = (*it)->getFamily();
214 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
215 +            }
216 +            interactions_[key].insert(repulsivePower_);
217 +            vdwExplicit = true;
218 +          }
219            
220 +          
221            if (nbiType->isEAM()) {
222              // We found an explicit EAM interaction.  
223              // override all other metallic entries for this pair of atom types:
# Line 280 | Line 281 | namespace OpenMD {
281      }
282      
283      
284 <    // make sure every pair of atom types in this simulation has a
285 <    // non-bonded interaction:
284 >    // Make sure every pair of atom types in this simulation has a
285 >    // non-bonded interaction.  If not, just inform the user.
286  
287      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
288      set<AtomType*>::iterator it, jt;
289 +
290      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
291        atype1 = (*it);
292 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
292 >      for (jt = it; jt != simTypes.end(); ++jt) {
293          atype2 = (*jt);
294          key = make_pair(atype1, atype2);
295          
296          if (interactions_[key].size() == 0) {
297            sprintf( painCave.errMsg,
298 <                   "InteractionManager unable to find an appropriate non-bonded\n"
299 <                   "\tinteraction for atom types %s - %s\n",
298 >                   "InteractionManager could not find a matching non-bonded\n"
299 >                   "\tinteraction for atom types %s - %s\n"
300 >                   "\tProceeding without this interaction.\n",
301                     atype1->getName().c_str(), atype2->getName().c_str());
302            painCave.severity = OPENMD_INFO;
303 <          painCave.isFatal = 1;
303 >          painCave.isFatal = 0;
304            simError();
305          }
306        }
307      }
308  
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 –
309      initialized_ = true;
316 –  }
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 –    }
369 –
370 –    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 –    }
310    }
311  
312 <
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 <    }          
312 >  void InteractionManager::setCutoffRadius(RealType rcut) {
313      
314 <    if (simParams_->haveSwitchingFunctionType()) {
315 <      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_);
314 >    electrostatic_->setCutoffRadius(rcut);
315 >    eam_->setCutoffRadius(rcut);
316    }
317  
461 –  /**
462 –   * 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_;
485 –  }
486 –
487 –
318    void InteractionManager::doPrePair(InteractionData idat){
319      
320      if (!initialized_) initialize();
321          
322 +    // excluded interaction, so just return
323 +    if (idat.excluded) return;
324 +
325      set<NonBondedInteraction*>::iterator it;
326  
327 <    for (it = interactions_[ *(idat.atypes) ].begin();
328 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
327 >    for (it = interactions_[ idat.atypes ].begin();
328 >         it != interactions_[ idat.atypes ].end(); ++it){
329        if ((*it)->getFamily() == METALLIC_FAMILY) {
330          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
331        }
# Line 520 | Line 353 | namespace OpenMD {
353    void InteractionManager::doPair(InteractionData idat){
354      
355      if (!initialized_) initialize();
356 <  
356 >
357      set<NonBondedInteraction*>::iterator it;
358  
359 <    for (it = interactions_[ *(idat.atypes) ].begin();
360 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
528 <      (*it)->calcForce(idat);
529 <    
530 <    return;    
531 <  }
359 >    for (it = interactions_[ idat.atypes ].begin();
360 >         it != interactions_[ idat.atypes ].end(); ++it) {
361  
362 <  void InteractionManager::doSkipCorrection(InteractionData idat){
362 >      // electrostatics still has to worry about indirect
363 >      // contributions from excluded pairs of atoms:
364  
365 <    if (!initialized_) initialize();  
366 <    
537 <    set<NonBondedInteraction*>::iterator it;
538 <
539 <    for (it = interactions_[ *(idat.atypes) ].begin();
540 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
541 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
542 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
365 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
366 >        (*it)->calcForce(idat);
367        }
368      }
369      
# Line 564 | Line 388 | namespace OpenMD {
388  
389    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
390      if (!initialized_) initialize();
391 <    
391 >
392      AtomType* atype = typeMap_[*atid];
393  
394      pair<AtomType*, AtomType*> key = make_pair(atype, atype);

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