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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1576 by gezelter, Wed Jun 8 16:05:07 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 89 | Line 70 | namespace OpenMD {
70      electrostatic_->setForceField(forceField_);
71      maw_->setForceField(forceField_);
72  
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 –
73      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
74      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
75      AtomType* atype1;
# Line 302 | Line 263 | namespace OpenMD {
263          }
264        }
265      }
305 –
306 –    setupCutoffs();
307 –    setupSwitching();
308 –    setupNeighborlists();
266  
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 –
267      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 –    }
268    }
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 –    }          
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_);
459 –  }
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();    
269    
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 –
270    void InteractionManager::doPrePair(InteractionData idat){
271      
272      if (!initialized_) initialize();
273          
274      set<NonBondedInteraction*>::iterator it;
275  
276 <    for (it = interactions_[ *(idat.atypes) ].begin();
277 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
276 >    for (it = interactions_[ idat.atypes ].begin();
277 >         it != interactions_[ idat.atypes ].end(); ++it){
278        if ((*it)->getFamily() == METALLIC_FAMILY) {
279          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
280        }
# Line 523 | Line 305 | namespace OpenMD {
305    
306      set<NonBondedInteraction*>::iterator it;
307  
308 <    for (it = interactions_[ *(idat.atypes) ].begin();
309 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
308 >    for (it = interactions_[ idat.atypes ].begin();
309 >         it != interactions_[ idat.atypes ].end(); ++it)
310        (*it)->calcForce(idat);
311      
312      return;    
# Line 536 | Line 318 | namespace OpenMD {
318      
319      set<NonBondedInteraction*>::iterator it;
320  
321 <    for (it = interactions_[ *(idat.atypes) ].begin();
322 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
321 >    for (it = interactions_[ idat.atypes ].begin();
322 >         it != interactions_[ idat.atypes ].end(); ++it){
323        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
324          dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
325        }

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