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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 1568 by gezelter, Wed May 25 16:20:37 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 <  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  
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 –
270      initialized_ = true;
271    }
272 <  
273 <  /**
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() {
272 >
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274      
275 <    Globals* simParams_ = info_->getSimParams();
276 <    
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 <    }
275 >    electrostatic_->setCutoffRadius(rcut);
276 >    eam_->setCutoffRadius(rcut);
277    }
278  
279 <
280 <  /**
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_);
279 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
280 >    electrostatic_->setSwitchingRadius(rswitch);
281    }
282 <
282 >  
283    void InteractionManager::doPrePair(InteractionData idat){
284 <    
285 <    if (!initialized_) initialize();
284 >        printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
285 > /*    if (!initialized_) initialize();
286          
287 +    // excluded interaction, so just return
288 +    if (idat.excluded) return;
289 +
290      set<NonBondedInteraction*>::iterator it;
291  
292 <    for (it = interactions_[ *(idat.atypes) ].begin();
293 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
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 <    }
297 >    }*/
298      
299      return;    
300    }
301    
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 +    wrapData(idatThread, idat);
312 +
313 +    set<NonBondedInteraction*>::iterator it;
314 +
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;
323 +  }
324 +
325    void InteractionManager::doPreForce(SelfData sdat){
326  
327      if (!initialized_) initialize();
# Line 487 | 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();  
505 <    
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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