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root/OpenMD/branches/devel_omp/src/nonbonded/InteractionManager.cpp
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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.
branches/devel_omp/src/nonbonded/InteractionManager.cpp (file contents), Revision 1608 by mciznick, Tue Aug 9 01:58:56 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 86 | 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_);
91 –
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
73  
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 –
74      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76      AtomType* atype1;
# Line 280 | 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();
308 <    setupNeighborlists();
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);
276 <    //notifyFortranSkinThickness(&skinThickness_);
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274 >    
275 >    electrostatic_->setCutoffRadius(rcut);
276 >    eam_->setCutoffRadius(rcut);
277 >  }
278  
279 <    initialized_ = true;
279 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
280 >    electrostatic_->setSwitchingRadius(rswitch);
281    }
282    
283 <  /**
284 <   * setupCutoffs
285 <   *
286 <   * Sets the values of cutoffRadius and cutoffMethod
287 <   *
288 <   * 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 <    }
283 >  void InteractionManager::doPrePair(InteractionData idat){
284 >        printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
285 > /*    if (!initialized_) initialize();
286 >        
287 >    // excluded interaction, so just return
288 >    if (idat.excluded) return;
289  
290 <    map<string, CutoffMethod> stringToCutoffMethod;
291 <    stringToCutoffMethod["HARD"] = HARD;
292 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
293 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
294 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
295 <  
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;
290 >    set<NonBondedInteraction*>::iterator it;
291 >
292 >    for (it = interactions_[ idat.atypes ].begin();
293 >         it != interactions_[ idat.atypes ].end(); ++it){
294 >      if ((*it)->getFamily() == METALLIC_FAMILY) {
295 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
296        }
297 <    } else {
298 <      sprintf(painCave.errMsg,
299 <              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
300 <              "\tOpenMD will use SHIFTED_FORCE.\n");
396 <        painCave.isFatal = 0;
397 <        painCave.severity = OPENMD_INFO;
398 <        simError();
399 <        cutoffMethod_ = SHIFTED_FORCE;        
400 <    }
401 <  }
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();    
297 >    }*/
298 >    
299 >    return;    
300 >  }
301    
302 <    if (simParams_->haveSkinThickness()) {
303 <      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_;
302 >  void InteractionManager::initializeOMP() {
303 >        if (!initialized_) initialize();
304    }
305  
306 +  void InteractionManager::doPrePairOMP(InteractionDataPrv idatThread){
307 +        InteractionData idat;
308 +    // excluded interaction, so just return
309 +    if (idat.excluded) return;
310  
311 <  void InteractionManager::doPrePair(InteractionData idat){
312 <    
490 <    if (!initialized_) initialize();
491 <        
311 >    wrapData(idatThread, idat);
312 >
313      set<NonBondedInteraction*>::iterator it;
314  
315 <    for (it = interactions_[ *(idat.atypes) ].begin();
316 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
315 >    for (it = interactions_[ idat.atypes ].begin();
316 >         it != interactions_[ idat.atypes ].end(); ++it){
317        if ((*it)->getFamily() == METALLIC_FAMILY) {
318          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
319        }
320      }
321 <    
322 <    return;    
321 >
322 >    return;
323    }
324 <  
324 >
325    void InteractionManager::doPreForce(SelfData sdat){
326  
327      if (!initialized_) initialize();
# Line 518 | Line 339 | namespace OpenMD {
339    }
340  
341    void InteractionManager::doPair(InteractionData idat){
342 <    
343 <    if (!initialized_) initialize();
344 <  
342 >        printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
343 >    /*if (!initialized_) initialize();
344 >
345      set<NonBondedInteraction*>::iterator it;
346  
347 <    for (it = interactions_[ *(idat.atypes) ].begin();
348 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
349 <      (*it)->calcForce(idat);
347 >    for (it = interactions_[ idat.atypes ].begin();
348 >         it != interactions_[ idat.atypes ].end(); ++it) {
349 >
350 >      // electrostatics still has to worry about indirect
351 >      // contributions from excluded pairs of atoms:
352 >
353 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
354 >        (*it)->calcForce(idat);
355 >      }
356 >    }*/
357      
358      return;    
359    }
360  
361 <  void InteractionManager::doSkipCorrection(InteractionData idat){
361 >  void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) {
362 >        dst.A1 = src.A1;
363 >        dst.A2 = src.A2;
364 >        dst.atypes = src.atypes;
365 >        dst.d = &src.d;
366 >        dst.dfrho1 = src.dfrho1;
367 >        dst.dfrho2 = src.dfrho2;
368 >        dst.eFrame1 = src.eFrame1;
369 >        dst.eFrame2 = src.eFrame2;
370 >        dst.electroMult = &src.electroMult;
371 >        dst.excluded = src.excluded;
372 >        dst.f1 = &src.f1;
373 >        dst.frho1 = src.frho1;
374 >        dst.frho2 = src.frho2;
375 >        dst.particlePot1 = src.particlePot1;
376 >        dst.particlePot2 = src.particlePot2;
377 >        dst.pot = &src.pot;
378 >        dst.r2 = &src.r2;
379 >        dst.rcut = &src.rcut;
380 >        dst.rho1 = src.rho1;
381 >        dst.rho2 = src.rho2;
382 >        dst.rij = &src.rij;
383 >        dst.shiftedForce = src.shiftedForce;
384 >        dst.shiftedPot = src.shiftedPot;
385 >        dst.skippedCharge1 = src.skippedCharge1;
386 >        dst.skippedCharge2 = src.skippedCharge2;
387 >        dst.sw = &src.sw;
388 >        dst.t1 = src.t1;
389 >        dst.t2 = src.t2;
390 >        dst.topoDist = src.topoDist;
391 >        dst.vdwMult = &src.vdwMult;
392 >        dst.vpair = &src.vpair;
393 >  }
394  
395 <    if (!initialized_) initialize();  
536 <    
395 >  void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
396      set<NonBondedInteraction*>::iterator it;
397 +    InteractionData idat;
398  
399 <    for (it = interactions_[ *(idat.atypes) ].begin();
400 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
401 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
402 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
399 >    wrapData(idatThread, idat);
400 >
401 >    for (it = interactions_[ idat.atypes ].begin();
402 >         it != interactions_[ idat.atypes ].end(); ++it) {
403 >
404 >      // electrostatics still has to worry about indirect
405 >      // contributions from excluded pairs of atoms:
406 >
407 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
408 >        (*it)->calcForce(idat);
409        }
410      }
411 <    
412 <    return;    
411 >
412 >    return;
413    }
414  
415    void InteractionManager::doSelfCorrection(SelfData sdat){

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