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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1586 by gezelter, Tue Jun 21 06:34:35 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 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
51 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
52 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
53 <  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
54 <
55 <  map<int, AtomType*> InteractionManager::typeMap_;
56 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
57 <
60 <  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;
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 84 | 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  
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 –
74      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76      AtomType* atype1;
# Line 278 | 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  
270 <    setupCutoffs();
271 <    setupSwitching();
270 >    initialized_ = true;
271 >  }
272  
273 <    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
274 <    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
275 <    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274 >    electrostatic_->setCutoffRadius(rcut);
275 >    eam_->setCutoffRadius(rcut);
276 >  }
277  
278 <    initialized_ = true;
278 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
279 >    electrostatic_->setSwitchingRadius(rswitch);
280    }
281    
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 –    }
397 –  }
398 –
399 –
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 –    }          
430 –    
431 –    if (simParams_->haveSwitchingFunctionType()) {
432 –      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_);
455 –  }
456 –
282    void InteractionManager::doPrePair(InteractionData idat){
283      
284      if (!initialized_) initialize();
285          
286      set<NonBondedInteraction*>::iterator it;
287  
288 <    for (it = interactions_[ *(idat.atypes) ].begin();
289 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
288 >    for (it = interactions_[ idat.atypes ].begin();
289 >         it != interactions_[ idat.atypes ].end(); ++it){
290        if ((*it)->getFamily() == METALLIC_FAMILY) {
291          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
292        }
# Line 492 | Line 317 | namespace OpenMD {
317    
318      set<NonBondedInteraction*>::iterator it;
319  
320 <    for (it = interactions_[ *(idat.atypes) ].begin();
321 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
320 >    for (it = interactions_[ idat.atypes ].begin();
321 >         it != interactions_[ idat.atypes ].end(); ++it)
322        (*it)->calcForce(idat);
323      
324      return;    
# Line 502 | Line 327 | namespace OpenMD {
327    void InteractionManager::doSkipCorrection(InteractionData idat){
328  
329      if (!initialized_) initialize();  
330 <    
330 >
331      set<NonBondedInteraction*>::iterator it;
332  
333 <    for (it = interactions_[ *(idat.atypes) ].begin();
334 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
333 >    for (it = interactions_[ idat.atypes ].begin();
334 >         it != interactions_[ idat.atypes ].end(); ++it){
335        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
336          dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
337        }

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