ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/nonbonded/InteractionManager.cpp
(Generate patch)

Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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"
43 – #include "UseTheForce/doForces_interface.h"
44  
45   namespace OpenMD {
46  
47 <  InteractionManager* InteractionManager::_instance = NULL;
48 <  SimInfo* InteractionManager::info_ = NULL;
49 <  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_;
62 <
63 <  LJ* InteractionManager::lj_ = new LJ();
64 <  GB* InteractionManager::gb_ = new GB();
65 <  Sticky* InteractionManager::sticky_ = new Sticky();
66 <  Morse* InteractionManager::morse_ = new Morse();
67 <  EAM* InteractionManager::eam_ = new EAM();
68 <  SC* InteractionManager::sc_ = new SC();
69 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
70 <  MAW* InteractionManager::maw_ = new MAW();
71 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
72 <
73 <  InteractionManager* InteractionManager::Instance() {
74 <    if (!_instance) {
75 <      _instance = new InteractionManager();
76 <    }
77 <    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() {
63 <    
63 >
64 >    if (initialized_) return;
65 >
66      ForceField* forceField_ = info_->getForceField();
67      
68      lj_->setForceField(forceField_);
# Line 87 | Line 71 | namespace OpenMD {
71      eam_->setForceField(forceField_);
72      sc_->setForceField(forceField_);
73      morse_->setForceField(forceField_);
74 +    electrostatic_->setSimInfo(info_);
75      electrostatic_->setForceField(forceField_);
76      maw_->setForceField(forceField_);
77 +    repulsivePower_->setForceField(forceField_);
78  
93 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
94 –
95 –    // Force fields can set options on how to scale van der Waals and electrostatic
96 –    // interactions for atoms connected via bonds, bends and torsions
97 –    // in this case the topological distance between atoms is:
98 –    // 0 = topologically unconnected
99 –    // 1 = bonded together
100 –    // 2 = connected via a bend
101 –    // 3 = connected via a torsion
102 –
103 –    vdwScale_[0] = 1.0;
104 –    vdwScale_[1] = fopts.getvdw12scale();
105 –    vdwScale_[2] = fopts.getvdw13scale();
106 –    vdwScale_[3] = fopts.getvdw14scale();
107 –
108 –    electrostaticScale_[0] = 1.0;
109 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
110 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112 –
79      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
80      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
81      AtomType* atype1;
# Line 121 | Line 87 | namespace OpenMD {
87           atype1 = atomTypes->nextType(i1)) {
88        
89        // add it to the map:
124 –      AtomTypeProperties atp = atype1->getATP();    
90        
91        pair<map<int,AtomType*>::iterator,bool> ret;    
92 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
92 >      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
93        if (ret.second == false) {
94          sprintf( painCave.errMsg,
95                   "InteractionManager already had a previous entry with ident %d\n",
96 <                 atp.ident);
96 >                 atype1->getIdent());
97          painCave.severity = OPENMD_INFO;
98          painCave.isFatal = 0;
99          simError();                
# Line 146 | Line 111 | namespace OpenMD {
111          
112          bool vdwExplicit = false;
113          bool metExplicit = false;
114 <        bool hbExplicit = false;
114 >        // bool hbExplicit = false;
115                        
116          key = make_pair(atype1, atype2);
117          
# Line 215 | Line 180 | namespace OpenMD {
180                if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
181              }
182              interactions_[key].insert(morse_);
183 +            vdwExplicit = true;
184 +          }
185 +
186 +          if (nbiType->isRepulsivePower()) {
187 +            if (vdwExplicit) {
188 +              sprintf( painCave.errMsg,
189 +                       "InteractionManager::initialize found more than one "
190 +                       "explicit \n"
191 +                       "\tvan der Waals interaction for atom types %s - %s\n",
192 +                       atype1->getName().c_str(), atype2->getName().c_str());
193 +              painCave.severity = OPENMD_ERROR;
194 +              painCave.isFatal = 1;
195 +              simError();
196 +            }
197 +            // We found an explicit RepulsivePower interaction.  
198 +            // override all other vdw entries for this pair of atom types:
199 +            set<NonBondedInteraction*>::iterator it;
200 +            for (it = interactions_[key].begin();
201 +                 it != interactions_[key].end(); ++it) {
202 +              InteractionFamily ifam = (*it)->getFamily();
203 +              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 +            }
205 +            interactions_[key].insert(repulsivePower_);
206              vdwExplicit = true;
207            }
208            
209 +          
210            if (nbiType->isEAM()) {
211              // We found an explicit EAM interaction.  
212              // override all other metallic entries for this pair of atom types:
# Line 281 | Line 270 | namespace OpenMD {
270      }
271      
272      
273 <    // make sure every pair of atom types in this simulation has a
274 <    // non-bonded interaction:
273 >    // Make sure every pair of atom types in this simulation has a
274 >    // non-bonded interaction.  If not, just inform the user.
275  
276      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
277      set<AtomType*>::iterator it, jt;
278 +
279      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
280        atype1 = (*it);
281 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
281 >      for (jt = it; jt != simTypes.end(); ++jt) {
282          atype2 = (*jt);
283          key = make_pair(atype1, atype2);
284          
285          if (interactions_[key].size() == 0) {
286            sprintf( painCave.errMsg,
287 <                   "InteractionManager unable to find an appropriate non-bonded\n"
288 <                   "\tinteraction for atom types %s - %s\n",
287 >                   "InteractionManager could not find a matching non-bonded\n"
288 >                   "\tinteraction for atom types %s - %s\n"
289 >                   "\tProceeding without this interaction.\n",
290                     atype1->getName().c_str(), atype2->getName().c_str());
291            painCave.severity = OPENMD_INFO;
292 <          painCave.isFatal = 1;
292 >          painCave.isFatal = 0;
293            simError();
294          }
295        }
296      }
297  
307 –    setupCutoffs();
308 –    setupSwitching();
309 –    setupNeighborlists();
310 –
311 –    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
312 –    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
313 –    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
314 –    //notifyFortranSkinThickness(&skinThickness_);
315 –
298      initialized_ = true;
317 –  }
318 –  
319 –  /**
320 –   * setupCutoffs
321 –   *
322 –   * Sets the values of cutoffRadius and cutoffMethod
323 –   *
324 –   * cutoffRadius : realType
325 –   *  If the cutoffRadius was explicitly set, use that value.
326 –   *  If the cutoffRadius was not explicitly set:
327 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
328 –   *      No electrostatic atoms?  Poll the atom types present in the
329 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
330 –   *      Use the maximum suggested value that was found.
331 –   *
332 –   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
333 –   *      If cutoffMethod was explicitly set, use that choice.
334 –   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
335 –   */
336 –  void InteractionManager::setupCutoffs() {
337 –    
338 –    Globals* simParams_ = info_->getSimParams();
339 –    
340 –    if (simParams_->haveCutoffRadius()) {
341 –      rCut_ = simParams_->getCutoffRadius();
342 –    } else {      
343 –      if (info_->usesElectrostaticAtoms()) {
344 –        sprintf(painCave.errMsg,
345 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
346 –                "\tOpenMD will use a default value of 12.0 angstroms"
347 –                "\tfor the cutoffRadius.\n");
348 –        painCave.isFatal = 0;
349 –        painCave.severity = OPENMD_INFO;
350 –        simError();
351 –        rCut_ = 12.0;
352 –      } else {
353 –        RealType thisCut;
354 –        set<AtomType*>::iterator i;
355 –        set<AtomType*> atomTypes;
356 –        atomTypes = info_->getSimulatedAtomTypes();        
357 –        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
358 –          thisCut = getSuggestedCutoffRadius((*i));
359 –          rCut_ = max(thisCut, rCut_);
360 –        }
361 –        sprintf(painCave.errMsg,
362 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
363 –                "\tOpenMD will use %lf angstroms.\n",
364 –                rCut_);
365 –        painCave.isFatal = 0;
366 –        painCave.severity = OPENMD_INFO;
367 –        simError();
368 –      }            
369 –    }
370 –
371 –    map<string, CutoffMethod> stringToCutoffMethod;
372 –    stringToCutoffMethod["HARD"] = HARD;
373 –    stringToCutoffMethod["SWITCHED"] = SWITCHED;
374 –    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
375 –    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
376 –  
377 –    if (simParams_->haveCutoffMethod()) {
378 –      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
379 –      map<string, CutoffMethod>::iterator i;
380 –      i = stringToCutoffMethod.find(cutMeth);
381 –      if (i == stringToCutoffMethod.end()) {
382 –        sprintf(painCave.errMsg,
383 –                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
384 –                "\tShould be one of: "
385 –                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
386 –                cutMeth.c_str());
387 –        painCave.isFatal = 1;
388 –        painCave.severity = OPENMD_ERROR;
389 –        simError();
390 –      } else {
391 –        cutoffMethod_ = i->second;
392 –      }
393 –    } else {
394 –      sprintf(painCave.errMsg,
395 –              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
396 –              "\tOpenMD will use SHIFTED_FORCE.\n");
397 –        painCave.isFatal = 0;
398 –        painCave.severity = OPENMD_INFO;
399 –        simError();
400 –        cutoffMethod_ = SHIFTED_FORCE;        
401 –    }
299    }
300  
301 <
405 <  /**
406 <   * setupSwitching
407 <   *
408 <   * Sets the values of switchingRadius and
409 <   *  If the switchingRadius was explicitly set, use that value (but check it)
410 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
411 <   */
412 <  void InteractionManager::setupSwitching() {
413 <    Globals* simParams_ = info_->getSimParams();
414 <
415 <    if (simParams_->haveSwitchingRadius()) {
416 <      rSwitch_ = simParams_->getSwitchingRadius();
417 <      if (rSwitch_ > rCut_) {        
418 <        sprintf(painCave.errMsg,
419 <                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
420 <                rSwitch_, rCut_);
421 <        painCave.isFatal = 1;
422 <        painCave.severity = OPENMD_ERROR;
423 <        simError();
424 <      }
425 <    } else {      
426 <      rSwitch_ = 0.85 * rCut_;
427 <      sprintf(painCave.errMsg,
428 <              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
429 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
430 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
431 <      painCave.isFatal = 0;
432 <      painCave.severity = OPENMD_WARNING;
433 <      simError();
434 <    }          
301 >  void InteractionManager::setCutoffRadius(RealType rcut) {
302      
303 <    if (simParams_->haveSwitchingFunctionType()) {
304 <      string funcType = simParams_->getSwitchingFunctionType();
438 <      toUpper(funcType);
439 <      if (funcType == "CUBIC") {
440 <        sft_ = cubic;
441 <      } else {
442 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
443 <          sft_ = fifth_order_poly;
444 <        } else {
445 <          // throw error        
446 <          sprintf( painCave.errMsg,
447 <                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
448 <                   "\tswitchingFunctionType must be one of: "
449 <                   "\"cubic\" or \"fifth_order_polynomial\".",
450 <                   funcType.c_str() );
451 <          painCave.isFatal = 1;
452 <          painCave.severity = OPENMD_ERROR;
453 <          simError();
454 <        }          
455 <      }
456 <    }
457 <
458 <    switcher_->setSwitchType(sft_);
459 <    switcher_->setSwitch(rSwitch_, rCut_);
303 >    electrostatic_->setCutoffRadius(rcut);
304 >    eam_->setCutoffRadius(rcut);
305    }
306  
462 –  /**
463 –   * setupNeighborlists
464 –   *
465 –   *  If the skinThickness was explicitly set, use that value (but check it)
466 –   *  If the skinThickness was not explicitly set: use 1.0 angstroms
467 –   */
468 –  void InteractionManager::setupNeighborlists() {  
469 –
470 –    Globals* simParams_ = info_->getSimParams();    
471 –  
472 –    if (simParams_->haveSkinThickness()) {
473 –      skinThickness_ = simParams_->getSkinThickness();
474 –    } else {      
475 –      skinThickness_ = 1.0;
476 –      sprintf(painCave.errMsg,
477 –              "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n"
478 –              "\tOpenMD will use a default value of %f Angstroms\n"
479 –              "\tfor this simulation\n", skinThickness_);
480 –      painCave.severity = OPENMD_INFO;
481 –      painCave.isFatal = 0;
482 –      simError();
483 –    }            
484 –
485 –    listRadius_ = rCut_ + skinThickness_;
486 –  }
487 –
488 –
307    void InteractionManager::doPrePair(InteractionData idat){
308      
309      if (!initialized_) initialize();
310          
311 +    // excluded interaction, so just return
312 +    if (idat.excluded) return;
313 +
314      set<NonBondedInteraction*>::iterator it;
315  
316 <    for (it = interactions_[idat.atypes].begin();
317 <         it != interactions_[idat.atypes].end(); ++it){
316 >    for (it = interactions_[ idat.atypes ].begin();
317 >         it != interactions_[ idat.atypes ].end(); ++it){
318        if ((*it)->getFamily() == METALLIC_FAMILY) {
319          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
320        }
# Line 521 | Line 342 | namespace OpenMD {
342    void InteractionManager::doPair(InteractionData idat){
343      
344      if (!initialized_) initialize();
345 <  
345 >
346      set<NonBondedInteraction*>::iterator it;
347  
348 <    for (it = interactions_[idat.atypes].begin();
349 <         it != interactions_[idat.atypes].end(); ++it)
529 <      (*it)->calcForce(idat);
530 <    
531 <    return;    
532 <  }
348 >    for (it = interactions_[ idat.atypes ].begin();
349 >         it != interactions_[ idat.atypes ].end(); ++it) {
350  
351 <  void InteractionManager::doSkipCorrection(InteractionData idat){
351 >      // electrostatics still has to worry about indirect
352 >      // contributions from excluded pairs of atoms:
353  
354 <    if (!initialized_) initialize();  
355 <    
538 <    set<NonBondedInteraction*>::iterator it;
539 <
540 <    for (it = interactions_[idat.atypes].begin();
541 <         it != interactions_[idat.atypes].end(); ++it){
542 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
543 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
354 >      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
355 >        (*it)->calcForce(idat);
356        }
357      }
358      
# Line 565 | Line 377 | namespace OpenMD {
377  
378    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
379      if (!initialized_) initialize();
380 <    
380 >
381      AtomType* atype = typeMap_[*atid];
382  
383      pair<AtomType*, AtomType*> key = make_pair(atype, atype);

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines