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Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

# Line 36 | Line 36
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).                        
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 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
52 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
53 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
54 <  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
55 <
56 <  map<int, AtomType*> InteractionManager::typeMap_;
57 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
58 <
59 <  LJ* InteractionManager::lj_ = new LJ();
61 <  GB* InteractionManager::gb_ = new GB();
62 <  Sticky* InteractionManager::sticky_ = new Sticky();
63 <  Morse* InteractionManager::morse_ = new Morse();
64 <  EAM* InteractionManager::eam_ = new EAM();
65 <  SC* InteractionManager::sc_ = new SC();
66 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
67 <  MAW* InteractionManager::maw_ = new MAW();
68 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
69 <
70 <  InteractionManager* InteractionManager::Instance() {
71 <    if (!_instance) {
72 <      _instance = new InteractionManager();
73 <    }
74 <    return _instance;
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    void InteractionManager::initialize() {
63 <    
63 >
64 >    if (initialized_) return;
65 >
66      ForceField* forceField_ = info_->getForceField();
67      
68      lj_->setForceField(forceField_);
# Line 84 | Line 71 | namespace OpenMD {
71      eam_->setForceField(forceField_);
72      sc_->setForceField(forceField_);
73      morse_->setForceField(forceField_);
74 +    electrostatic_->setSimInfo(info_);
75      electrostatic_->setForceField(forceField_);
76      maw_->setForceField(forceField_);
77 +    repulsivePower_->setForceField(forceField_);
78  
90 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
91 –
92 –    // Force fields can set options on how to scale van der Waals and electrostatic
93 –    // interactions for atoms connected via bonds, bends and torsions
94 –    // in this case the topological distance between atoms is:
95 –    // 0 = topologically unconnected
96 –    // 1 = bonded together
97 –    // 2 = connected via a bend
98 –    // 3 = connected via a torsion
99 –
100 –    vdwScale_[0] = 1.0;
101 –    vdwScale_[1] = fopts.getvdw12scale();
102 –    vdwScale_[2] = fopts.getvdw13scale();
103 –    vdwScale_[3] = fopts.getvdw14scale();
104 –
105 –    electrostaticScale_[0] = 1.0;
106 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
107 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
108 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
109 –
79      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
80      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
81      AtomType* atype1;
# Line 118 | Line 87 | namespace OpenMD {
87           atype1 = atomTypes->nextType(i1)) {
88        
89        // add it to the map:
121 –      AtomTypeProperties atp = atype1->getATP();    
90        
91        pair<map<int,AtomType*>::iterator,bool> ret;    
92 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
92 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
93        if (ret.second == false) {
94          sprintf( painCave.errMsg,
95                   "InteractionManager already had a previous entry with ident %d\n",
96 <                 atp.ident);
96 >                 atype1->getIdent());
97          painCave.severity = OPENMD_INFO;
98          painCave.isFatal = 0;
99          simError();                
# Line 143 | Line 111 | namespace OpenMD {
111          
112          bool vdwExplicit = false;
113          bool metExplicit = false;
114 <        bool hbExplicit = false;
114 >        // bool hbExplicit = false;
115                        
116          key = make_pair(atype1, atype2);
117          
# Line 214 | Line 182 | namespace OpenMD {
182              interactions_[key].insert(morse_);
183              vdwExplicit = true;
184            }
185 +
186 +          if (nbiType->isRepulsivePower()) {
187 +            if (vdwExplicit) {
188 +              sprintf( painCave.errMsg,
189 +                       "InteractionManager::initialize found more than one "
190 +                       "explicit \n"
191 +                       "\tvan der Waals interaction for atom types %s - %s\n",
192 +                       atype1->getName().c_str(), atype2->getName().c_str());
193 +              painCave.severity = OPENMD_ERROR;
194 +              painCave.isFatal = 1;
195 +              simError();
196 +            }
197 +            // We found an explicit RepulsivePower interaction.  
198 +            // override all other vdw entries for this pair of atom types:
199 +            set<NonBondedInteraction*>::iterator it;
200 +            for (it = interactions_[key].begin();
201 +                 it != interactions_[key].end(); ++it) {
202 +              InteractionFamily ifam = (*it)->getFamily();
203 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 +            }
205 +            interactions_[key].insert(repulsivePower_);
206 +            vdwExplicit = true;
207 +          }
208            
209 +          
210            if (nbiType->isEAM()) {
211              // We found an explicit EAM interaction.  
212              // override all other metallic entries for this pair of atom types:
# Line 278 | Line 270 | namespace OpenMD {
270      }
271      
272      
273 <    // make sure every pair of atom types in this simulation has a
274 <    // non-bonded interaction:
273 >    // Make sure every pair of atom types in this simulation has a
274 >    // non-bonded interaction.  If not, just inform the user.
275  
276      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
277      set<AtomType*>::iterator it, jt;
278 +
279      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
280        atype1 = (*it);
281 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
281 >      for (jt = it; jt != simTypes.end(); ++jt) {
282          atype2 = (*jt);
283          key = make_pair(atype1, atype2);
284          
285          if (interactions_[key].size() == 0) {
286            sprintf( painCave.errMsg,
287 <                   "InteractionManager unable to find an appropriate non-bonded\n"
288 <                   "\tinteraction for atom types %s - %s\n",
287 >                   "InteractionManager could not find a matching non-bonded\n"
288 >                   "\tinteraction for atom types %s - %s\n"
289 >                   "\tProceeding without this interaction.\n",
290                     atype1->getName().c_str(), atype2->getName().c_str());
291            painCave.severity = OPENMD_INFO;
292 <          painCave.isFatal = 1;
292 >          painCave.isFatal = 0;
293            simError();
294          }
295        }
296      }
297  
304 –    setupCutoffs();
305 –    setupSwitching();
306 –
307 –    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
308 –    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
309 –    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
310 –
298      initialized_ = true;
312 –  }
313 –  
314 –  /**
315 –   * setupCutoffs
316 –   *
317 –   * Sets the values of cutoffRadius and cutoffMethod
318 –   *
319 –   * cutoffRadius : realType
320 –   *  If the cutoffRadius was explicitly set, use that value.
321 –   *  If the cutoffRadius was not explicitly set:
322 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
323 –   *      No electrostatic atoms?  Poll the atom types present in the
324 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
325 –   *      Use the maximum suggested value that was found.
326 –   *
327 –   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
328 –   *      If cutoffMethod was explicitly set, use that choice.
329 –   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
330 –   */
331 –  void InteractionManager::setupCutoffs() {
332 –    
333 –    Globals* simParams_ = info_->getSimParams();
334 –    
335 –    if (simParams_->haveCutoffRadius()) {
336 –      rCut_ = simParams_->getCutoffRadius();
337 –    } else {      
338 –      if (info_->usesElectrostaticAtoms()) {
339 –        sprintf(painCave.errMsg,
340 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
341 –                "\tOpenMD will use a default value of 12.0 angstroms"
342 –                "\tfor the cutoffRadius.\n");
343 –        painCave.isFatal = 0;
344 –        painCave.severity = OPENMD_INFO;
345 –        simError();
346 –        rCut_ = 12.0;
347 –      } else {
348 –        RealType thisCut;
349 –        set<AtomType*>::iterator i;
350 –        set<AtomType*> atomTypes;
351 –        atomTypes = info_->getSimulatedAtomTypes();        
352 –        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
353 –          thisCut = getSuggestedCutoffRadius((*i));
354 –          rCut_ = max(thisCut, rCut_);
355 –        }
356 –        sprintf(painCave.errMsg,
357 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
358 –                "\tOpenMD will use %lf angstroms.\n",
359 –                rCut_);
360 –        painCave.isFatal = 0;
361 –        painCave.severity = OPENMD_INFO;
362 –        simError();
363 –      }            
364 –    }
365 –
366 –    map<string, CutoffMethod> stringToCutoffMethod;
367 –    stringToCutoffMethod["HARD"] = HARD;
368 –    stringToCutoffMethod["SWITCHED"] = SWITCHED;
369 –    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
370 –    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
371 –  
372 –    if (simParams_->haveCutoffMethod()) {
373 –      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
374 –      map<string, CutoffMethod>::iterator i;
375 –      i = stringToCutoffMethod.find(cutMeth);
376 –      if (i == stringToCutoffMethod.end()) {
377 –        sprintf(painCave.errMsg,
378 –                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
379 –                "\tShould be one of: "
380 –                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
381 –                cutMeth.c_str());
382 –        painCave.isFatal = 1;
383 –        painCave.severity = OPENMD_ERROR;
384 –        simError();
385 –      } else {
386 –        cutoffMethod_ = i->second;
387 –      }
388 –    } else {
389 –      sprintf(painCave.errMsg,
390 –              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
391 –              "\tOpenMD will use SHIFTED_FORCE.\n");
392 –        painCave.isFatal = 0;
393 –        painCave.severity = OPENMD_INFO;
394 –        simError();
395 –        cutoffMethod_ = SHIFTED_FORCE;        
396 –    }
299    }
300  
301 <
400 <  /**
401 <   * setupSwitching
402 <   *
403 <   * Sets the values of switchingRadius and
404 <   *  If the switchingRadius was explicitly set, use that value (but check it)
405 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
406 <   */
407 <  void InteractionManager::setupSwitching() {
408 <    Globals* simParams_ = info_->getSimParams();
409 <
410 <    if (simParams_->haveSwitchingRadius()) {
411 <      rSwitch_ = simParams_->getSwitchingRadius();
412 <      if (rSwitch_ > rCut_) {        
413 <        sprintf(painCave.errMsg,
414 <                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
415 <                rSwitch_, rCut_);
416 <        painCave.isFatal = 1;
417 <        painCave.severity = OPENMD_ERROR;
418 <        simError();
419 <      }
420 <    } else {      
421 <      rSwitch_ = 0.85 * rCut_;
422 <      sprintf(painCave.errMsg,
423 <              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
424 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
425 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
426 <      painCave.isFatal = 0;
427 <      painCave.severity = OPENMD_WARNING;
428 <      simError();
429 <    }          
301 >  void InteractionManager::setCutoffRadius(RealType rcut) {
302      
303 <    if (simParams_->haveSwitchingFunctionType()) {
304 <      string funcType = simParams_->getSwitchingFunctionType();
433 <      toUpper(funcType);
434 <      if (funcType == "CUBIC") {
435 <        sft_ = cubic;
436 <      } else {
437 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
438 <          sft_ = fifth_order_poly;
439 <        } else {
440 <          // throw error        
441 <          sprintf( painCave.errMsg,
442 <                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
443 <                   "\tswitchingFunctionType must be one of: "
444 <                   "\"cubic\" or \"fifth_order_polynomial\".",
445 <                   funcType.c_str() );
446 <          painCave.isFatal = 1;
447 <          painCave.severity = OPENMD_ERROR;
448 <          simError();
449 <        }          
450 <      }
451 <    }
452 <
453 <    switcher_->setSwitchType(sft_);
454 <    switcher_->setSwitch(rSwitch_, rCut_);
303 >    electrostatic_->setCutoffRadius(rcut);
304 >    eam_->setCutoffRadius(rcut);
305    }
306  
307    void InteractionManager::doPrePair(InteractionData idat){
308      
309      if (!initialized_) initialize();
310          
311 +    // excluded interaction, so just return
312 +    if (idat.excluded) return;
313 +
314      set<NonBondedInteraction*>::iterator it;
315  
316 <    for (it = interactions_[ *(idat.atypes) ].begin();
317 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
316 >    for (it = interactions_[ idat.atypes ].begin();
317 >         it != interactions_[ idat.atypes ].end(); ++it){
318        if ((*it)->getFamily() == METALLIC_FAMILY) {
319          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
320        }
# Line 489 | Line 342 | namespace OpenMD {
342    void InteractionManager::doPair(InteractionData idat){
343      
344      if (!initialized_) initialize();
345 <  
345 >
346      set<NonBondedInteraction*>::iterator it;
347  
348 <    for (it = interactions_[ *(idat.atypes) ].begin();
349 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
497 <      (*it)->calcForce(idat);
498 <    
499 <    return;    
500 <  }
348 >    for (it = interactions_[ idat.atypes ].begin();
349 >         it != interactions_[ idat.atypes ].end(); ++it) {
350  
351 <  void InteractionManager::doSkipCorrection(InteractionData idat){
351 >      // electrostatics still has to worry about indirect
352 >      // contributions from excluded pairs of atoms:
353  
354 <    if (!initialized_) initialize();  
355 <    
506 <    set<NonBondedInteraction*>::iterator it;
507 <
508 <    for (it = interactions_[ *(idat.atypes) ].begin();
509 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
510 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
511 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
354 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
355 >        (*it)->calcForce(idat);
356        }
357      }
358      
# Line 533 | Line 377 | namespace OpenMD {
377  
378    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
379      if (!initialized_) initialize();
380 <    
380 >
381      AtomType* atype = typeMap_[*atid];
382  
383      pair<AtomType*, AtomType*> key = make_pair(atype, atype);

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