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Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 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 <  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};
57 <
58 <  map<int, AtomType*> InteractionManager::typeMap_;
59 <  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;
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() {
# Line 86 | Line 69 | namespace OpenMD {
69      eam_->setForceField(forceField_);
70      sc_->setForceField(forceField_);
71      morse_->setForceField(forceField_);
72 +    electrostatic_->setSimInfo(info_);
73      electrostatic_->setForceField(forceField_);
74      maw_->setForceField(forceField_);
75 +    repulsivePower_->setForceField(forceField_);
76  
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 –
77      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
78      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
79      AtomType* atype1;
# Line 120 | Line 85 | namespace OpenMD {
85           atype1 = atomTypes->nextType(i1)) {
86        
87        // add it to the map:
123 –      AtomTypeProperties atp = atype1->getATP();    
88        
89        pair<map<int,AtomType*>::iterator,bool> ret;    
90 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
90 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
91        if (ret.second == false) {
92          sprintf( painCave.errMsg,
93                   "InteractionManager already had a previous entry with ident %d\n",
94 <                 atp.ident);
94 >                 atype1->getIdent());
95          painCave.severity = OPENMD_INFO;
96          painCave.isFatal = 0;
97          simError();                
# Line 216 | Line 180 | namespace OpenMD {
180              interactions_[key].insert(morse_);
181              vdwExplicit = true;
182            }
183 +
184 +          if (nbiType->isRepulsivePower()) {
185 +            if (vdwExplicit) {
186 +              sprintf( painCave.errMsg,
187 +                       "InteractionManager::initialize found more than one "
188 +                       "explicit \n"
189 +                       "\tvan der Waals interaction for atom types %s - %s\n",
190 +                       atype1->getName().c_str(), atype2->getName().c_str());
191 +              painCave.severity = OPENMD_ERROR;
192 +              painCave.isFatal = 1;
193 +              simError();
194 +            }
195 +            // We found an explicit RepulsivePower interaction.  
196 +            // override all other vdw entries for this pair of atom types:
197 +            set<NonBondedInteraction*>::iterator it;
198 +            for (it = interactions_[key].begin();
199 +                 it != interactions_[key].end(); ++it) {
200 +              InteractionFamily ifam = (*it)->getFamily();
201 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
202 +            }
203 +            interactions_[key].insert(repulsivePower_);
204 +            vdwExplicit = true;
205 +          }
206            
207 +          
208            if (nbiType->isEAM()) {
209              // We found an explicit EAM interaction.  
210              // override all other metallic entries for this pair of atom types:
# Line 280 | Line 268 | namespace OpenMD {
268      }
269      
270      
271 <    // make sure every pair of atom types in this simulation has a
272 <    // non-bonded interaction:
271 >    // Make sure every pair of atom types in this simulation has a
272 >    // non-bonded interaction.  If not, just inform the user.
273  
274      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
275      set<AtomType*>::iterator it, jt;
276 +
277      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
278        atype1 = (*it);
279 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
279 >      for (jt = it; jt != simTypes.end(); ++jt) {
280          atype2 = (*jt);
281          key = make_pair(atype1, atype2);
282          
283          if (interactions_[key].size() == 0) {
284            sprintf( painCave.errMsg,
285 <                   "InteractionManager unable to find an appropriate non-bonded\n"
286 <                   "\tinteraction for atom types %s - %s\n",
285 >                   "InteractionManager could not find a matching non-bonded\n"
286 >                   "\tinteraction for atom types %s - %s\n"
287 >                   "\tProceeding without this interaction.\n",
288                     atype1->getName().c_str(), atype2->getName().c_str());
289            painCave.severity = OPENMD_INFO;
290 <          painCave.isFatal = 1;
290 >          painCave.isFatal = 0;
291            simError();
292          }
293        }
294      }
295  
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 –
296      initialized_ = true;
297    }
298 <  
299 <  /**
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() {
298 >
299 >  void InteractionManager::setCutoffRadius(RealType rcut) {
300      
301 <    Globals* simParams_ = info_->getSimParams();
302 <    
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 <    }
301 >    electrostatic_->setCutoffRadius(rcut);
302 >    eam_->setCutoffRadius(rcut);
303    }
304  
305 <
306 <  /**
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 <    }          
434 <    
435 <    if (simParams_->haveSwitchingFunctionType()) {
436 <      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_);
305 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
306 >    electrostatic_->setSwitchingRadius(rswitch);
307    }
460 –
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();    
308    
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 –
309    void InteractionManager::doPrePair(InteractionData idat){
310      
311      if (!initialized_) initialize();
312          
313 +    // excluded interaction, so just return
314 +    if (idat.excluded) return;
315 +
316      set<NonBondedInteraction*>::iterator it;
317  
318 <    for (it = interactions_[ *(idat.atypes) ].begin();
319 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
318 >    for (it = interactions_[ idat.atypes ].begin();
319 >         it != interactions_[ idat.atypes ].end(); ++it){
320        if ((*it)->getFamily() == METALLIC_FAMILY) {
321          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
322        }
# Line 520 | Line 344 | namespace OpenMD {
344    void InteractionManager::doPair(InteractionData idat){
345      
346      if (!initialized_) initialize();
347 <  
347 >
348      set<NonBondedInteraction*>::iterator it;
349  
350 <    for (it = interactions_[ *(idat.atypes) ].begin();
351 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
528 <      (*it)->calcForce(idat);
529 <    
530 <    return;    
531 <  }
350 >    for (it = interactions_[ idat.atypes ].begin();
351 >         it != interactions_[ idat.atypes ].end(); ++it) {
352  
353 <  void InteractionManager::doSkipCorrection(InteractionData idat){
353 >      // electrostatics still has to worry about indirect
354 >      // contributions from excluded pairs of atoms:
355  
356 <    if (!initialized_) initialize();  
357 <    
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);
356 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
357 >        (*it)->calcForce(idat);
358        }
359      }
360      

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