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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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"
44  
45   namespace OpenMD {
46  
47 <  InteractionManager* InteractionManager::_instance = NULL;
47 <  SimInfo* InteractionManager::info_ = NULL;
48 <  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};
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 <  map<int, AtomType*> InteractionManager::typeMap_;
63 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
64 <
65 <  LJ* InteractionManager::lj_ = new LJ();
66 <  GB* InteractionManager::gb_ = new GB();
67 <  Sticky* InteractionManager::sticky_ = new Sticky();
68 <  Morse* InteractionManager::morse_ = new Morse();
69 <  EAM* InteractionManager::eam_ = new EAM();
70 <  SC* InteractionManager::sc_ = new SC();
71 <  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;
62 >  InteractionManager::~InteractionManager() {
63 >    delete lj_;
64 >    delete gb_;
65 >    delete sticky_;
66 >    delete morse_;
67 >    delete repulsivePower_;
68 >    delete eam_;
69 >    delete sc_;
70 >    delete electrostatic_;
71 >    delete maw_;
72    }
73  
74    void InteractionManager::initialize() {
75 <    
75 >
76 >    if (initialized_) return;
77 >
78      ForceField* forceField_ = info_->getForceField();
79      
80      lj_->setForceField(forceField_);
# Line 86 | Line 83 | namespace OpenMD {
83      eam_->setForceField(forceField_);
84      sc_->setForceField(forceField_);
85      morse_->setForceField(forceField_);
86 +    electrostatic_->setSimInfo(info_);
87      electrostatic_->setForceField(forceField_);
88      maw_->setForceField(forceField_);
89 +    repulsivePower_->setForceField(forceField_);
90  
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 –
91      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92 +    int nTypes = atomTypes->size();
93 +    iHash_.resize(nTypes);
94 +    interactions_.resize(nTypes);
95      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
96      AtomType* atype1;
97      AtomType* atype2;
98 <    pair<AtomType*, AtomType*> key;
99 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
98 >    int atid1, atid2;
99 >
100 >    // We only need to worry about the types that are actually in the simulation:
101 >
102 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
103 >
104 >    lj_->setSimulatedAtomTypes(atypes);
105 >    gb_->setSimulatedAtomTypes(atypes);
106 >    sticky_->setSimulatedAtomTypes(atypes);
107 >    eam_->setSimulatedAtomTypes(atypes);
108 >    sc_->setSimulatedAtomTypes(atypes);
109 >    morse_->setSimulatedAtomTypes(atypes);
110 >    electrostatic_->setSimInfo(info_);
111 >    electrostatic_->setSimulatedAtomTypes(atypes);
112 >    maw_->setSimulatedAtomTypes(atypes);
113 >    repulsivePower_->setSimulatedAtomTypes(atypes);
114 >
115 >    set<AtomType*>::iterator at;
116 >
117 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
118      
119 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 <         atype1 = atomTypes->nextType(i1)) {
119 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 >      //   atype1 = atomTypes->nextType(i1)) {
121        
122 <      // add it to the map:
123 <      AtomTypeProperties atp = atype1->getATP();    
124 <      
122 >      atype1 = *at;
123 >      atid1 = atype1->getIdent();
124 >      iHash_[atid1].resize(nTypes);
125 >      interactions_[atid1].resize(nTypes);
126 >
127 >      // add it to the map:      
128        pair<map<int,AtomType*>::iterator,bool> ret;    
129 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
129 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
130        if (ret.second == false) {
131          sprintf( painCave.errMsg,
132                   "InteractionManager already had a previous entry with ident %d\n",
133 <                 atp.ident);
133 >                 atype1->getIdent());
134          painCave.severity = OPENMD_INFO;
135          painCave.isFatal = 0;
136          simError();                
# Line 139 | Line 142 | namespace OpenMD {
142      map<int, AtomType*>::iterator it1, it2;
143      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
144        atype1 = (*it1).second;
145 +      atid1 = atype1->getIdent();
146  
147        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
148          atype2 = (*it2).second;
149 +        atid2 = atype2->getIdent();
150 +                              
151 +        iHash_[atid1][atid2] = 0;
152          
146 –        bool vdwExplicit = false;
147 –        bool metExplicit = false;
148 –        bool hbExplicit = false;
149 –                      
150 –        key = make_pair(atype1, atype2);
151 –        
153          if (atype1->isLennardJones() && atype2->isLennardJones()) {
154 <          interactions_[key].insert(lj_);
154 >          interactions_[atid1][atid2].insert(lj_);
155 >          iHash_[atid1][atid2] |= LJ_PAIR;
156          }
157          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158 <          interactions_[key].insert(electrostatic_);
158 >          interactions_[atid1][atid2].insert(electrostatic_);
159 >          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
160          }
161          if (atype1->isSticky() && atype2->isSticky() ) {
162 <          interactions_[key].insert(sticky_);
162 >          interactions_[atid1][atid2].insert(sticky_);
163 >          iHash_[atid1][atid2] |= STICKY_PAIR;
164          }
165          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166 <          interactions_[key].insert(sticky_);
166 >          interactions_[atid1][atid2].insert(sticky_);
167 >          iHash_[atid1][atid2] |= STICKY_PAIR;
168          }
169          if (atype1->isEAM() && atype2->isEAM() ) {
170 <          interactions_[key].insert(eam_);
170 >          interactions_[atid1][atid2].insert(eam_);
171 >          iHash_[atid1][atid2] |= EAM_PAIR;
172          }
173          if (atype1->isSC() && atype2->isSC() ) {
174 <          interactions_[key].insert(sc_);
174 >          interactions_[atid1][atid2].insert(sc_);
175 >          iHash_[atid1][atid2] |= SC_PAIR;
176          }
177          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178 <          interactions_[key].insert(gb_);
178 >          interactions_[atid1][atid2].insert(gb_);
179 >          iHash_[atid1][atid2] |= GB_PAIR;
180          }
181          if ((atype1->isGayBerne() && atype2->isLennardJones())
182              || (atype1->isLennardJones() && atype2->isGayBerne())) {
183 <          interactions_[key].insert(gb_);
183 >          interactions_[atid1][atid2].insert(gb_);
184 >          iHash_[atid1][atid2] |= GB_PAIR;
185          }
186          
187          // look for an explicitly-set non-bonded interaction type using the
# Line 181 | Line 190 | namespace OpenMD {
190          
191          if (nbiType != NULL) {
192  
193 +          bool vdwExplicit = false;
194 +          bool metExplicit = false;
195 +          // bool hbExplicit = false;
196 +
197            if (nbiType->isLennardJones()) {
198              // We found an explicit Lennard-Jones interaction.  
199              // override all other vdw entries for this pair of atom types:
200              set<NonBondedInteraction*>::iterator it;
201 <            for (it = interactions_[key].begin();
202 <                 it != interactions_[key].end(); ++it) {
201 >            for (it = interactions_[atid1][atid2].begin();
202 >                 it != interactions_[atid1][atid2].end(); ++it) {
203                InteractionFamily ifam = (*it)->getFamily();
204 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 >              if (ifam == VANDERWAALS_FAMILY) {
205 >                interactions_[atid1][atid2].erase(*it);
206 >                iHash_[atid1][atid2] ^= (*it)->getHash();
207 >              }
208              }
209 <            interactions_[key].insert(lj_);
209 >            interactions_[atid1][atid2].insert(lj_);
210 >            iHash_[atid1][atid2] |= LJ_PAIR;
211              vdwExplicit = true;
212            }
213            
# Line 208 | Line 225 | namespace OpenMD {
225              // We found an explicit Morse interaction.  
226              // override all other vdw entries for this pair of atom types:
227              set<NonBondedInteraction*>::iterator it;
228 <            for (it = interactions_[key].begin();
229 <                 it != interactions_[key].end(); ++it) {
228 >            for (it = interactions_[atid1][atid2].begin();
229 >                 it != interactions_[atid1][atid2].end(); ++it) {
230                InteractionFamily ifam = (*it)->getFamily();
231 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
231 >              if (ifam == VANDERWAALS_FAMILY) {
232 >                interactions_[atid1][atid2].erase(*it);
233 >                iHash_[atid1][atid2] ^= (*it)->getHash();
234 >              }
235              }
236 <            interactions_[key].insert(morse_);
236 >            interactions_[atid1][atid2].insert(morse_);
237 >            iHash_[atid1][atid2] |= MORSE_PAIR;
238              vdwExplicit = true;
239            }
240 +
241 +          if (nbiType->isRepulsivePower()) {
242 +            if (vdwExplicit) {
243 +              sprintf( painCave.errMsg,
244 +                       "InteractionManager::initialize found more than one "
245 +                       "explicit \n"
246 +                       "\tvan der Waals interaction for atom types %s - %s\n",
247 +                       atype1->getName().c_str(), atype2->getName().c_str());
248 +              painCave.severity = OPENMD_ERROR;
249 +              painCave.isFatal = 1;
250 +              simError();
251 +            }
252 +            // We found an explicit RepulsivePower interaction.  
253 +            // override all other vdw entries for this pair of atom types:
254 +            set<NonBondedInteraction*>::iterator it;
255 +            for (it = interactions_[atid1][atid2].begin();
256 +                 it != interactions_[atid1][atid2].end(); ++it) {
257 +              InteractionFamily ifam = (*it)->getFamily();
258 +              if (ifam == VANDERWAALS_FAMILY) {
259 +                interactions_[atid1][atid2].erase(*it);
260 +                iHash_[atid1][atid2] ^= (*it)->getHash();
261 +              }
262 +            }
263 +            interactions_[atid1][atid2].insert(repulsivePower_);
264 +            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
265 +            vdwExplicit = true;
266 +          }
267            
268 +          
269            if (nbiType->isEAM()) {
270              // We found an explicit EAM interaction.  
271              // override all other metallic entries for this pair of atom types:
272              set<NonBondedInteraction*>::iterator it;
273 <            for (it = interactions_[key].begin();
274 <                 it != interactions_[key].end(); ++it) {
273 >            for (it = interactions_[atid1][atid2].begin();
274 >                 it != interactions_[atid1][atid2].end(); ++it) {
275                InteractionFamily ifam = (*it)->getFamily();
276 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
276 >              if (ifam == METALLIC_FAMILY) {
277 >                interactions_[atid1][atid2].erase(*it);
278 >                iHash_[atid1][atid2] ^= (*it)->getHash();
279 >              }
280              }
281 <            interactions_[key].insert(eam_);
281 >            interactions_[atid1][atid2].insert(eam_);
282 >            iHash_[atid1][atid2] |= EAM_PAIR;
283              metExplicit = true;
284            }
285            
# Line 244 | Line 297 | namespace OpenMD {
297              // We found an explicit Sutton-Chen interaction.  
298              // override all other metallic entries for this pair of atom types:
299              set<NonBondedInteraction*>::iterator it;
300 <            for (it = interactions_[key].begin();
301 <                 it != interactions_[key].end(); ++it) {
300 >            for (it = interactions_[atid1][atid2].begin();
301 >                 it != interactions_[atid1][atid2].end(); ++it) {
302                InteractionFamily ifam = (*it)->getFamily();
303 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
303 >              if (ifam == METALLIC_FAMILY) {
304 >                interactions_[atid1][atid2].erase(*it);
305 >                iHash_[atid1][atid2] ^= (*it)->getHash();
306 >              }
307              }
308 <            interactions_[key].insert(sc_);
308 >            interactions_[atid1][atid2].insert(sc_);
309 >            iHash_[atid1][atid2] |= SC_PAIR;
310              metExplicit = true;
311            }
312            
# Line 267 | Line 324 | namespace OpenMD {
324              // We found an explicit MAW interaction.  
325              // override all other vdw entries for this pair of atom types:
326              set<NonBondedInteraction*>::iterator it;
327 <            for (it = interactions_[key].begin();
328 <                 it != interactions_[key].end(); ++it) {
327 >            for (it = interactions_[atid1][atid2].begin();
328 >                 it != interactions_[atid1][atid2].end(); ++it) {
329                InteractionFamily ifam = (*it)->getFamily();
330 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
330 >              if (ifam == VANDERWAALS_FAMILY) {
331 >                interactions_[atid1][atid2].erase(*it);
332 >                iHash_[atid1][atid2] ^= (*it)->getHash();
333 >              }
334              }
335 <            interactions_[key].insert(maw_);
335 >            interactions_[atid1][atid2].insert(maw_);
336 >            iHash_[atid1][atid2] |= MAW_PAIR;
337              vdwExplicit = true;
338            }        
339          }
# Line 280 | Line 341 | namespace OpenMD {
341      }
342      
343      
344 <    // make sure every pair of atom types in this simulation has a
345 <    // non-bonded interaction:
344 >    // Make sure every pair of atom types in this simulation has a
345 >    // non-bonded interaction.  If not, just inform the user.
346  
347      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
348      set<AtomType*>::iterator it, jt;
349 +
350      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
351        atype1 = (*it);
352 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
352 >      atid1 = atype1->getIdent();
353 >      for (jt = it; jt != simTypes.end(); ++jt) {
354          atype2 = (*jt);
355 <        key = make_pair(atype1, atype2);
355 >        atid1 = atype1->getIdent();
356          
357 <        if (interactions_[key].size() == 0) {
357 >        if (interactions_[atid1][atid2].size() == 0) {
358            sprintf( painCave.errMsg,
359 <                   "InteractionManager unable to find an appropriate non-bonded\n"
360 <                   "\tinteraction for atom types %s - %s\n",
359 >                   "InteractionManager could not find a matching non-bonded\n"
360 >                   "\tinteraction for atom types %s - %s\n"
361 >                   "\tProceeding without this interaction.\n",
362                     atype1->getName().c_str(), atype2->getName().c_str());
363            painCave.severity = OPENMD_INFO;
364 <          painCave.isFatal = 1;
364 >          painCave.isFatal = 0;
365            simError();
366          }
367        }
368      }
369  
306 –    setupCutoffs();
307 –    setupSwitching();
308 –    setupNeighborlists();
309 –
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 –
370      initialized_ = true;
371    }
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 –    }
372  
373 <    map<string, CutoffMethod> stringToCutoffMethod;
374 <    stringToCutoffMethod["HARD"] = HARD;
375 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
376 <    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 <    }
373 >  void InteractionManager::setCutoffRadius(RealType rcut) {
374 >    
375 >    electrostatic_->setCutoffRadius(rcut);
376 >    eam_->setCutoffRadius(rcut);
377    }
378  
379 <
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 <    }          
379 >  void InteractionManager::doPrePair(InteractionData &idat){
380      
381 <    if (simParams_->haveSwitchingFunctionType()) {
382 <      string funcType = simParams_->getSwitchingFunctionType();
383 <      toUpper(funcType);
384 <      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 <    }
381 >    if (!initialized_) initialize();
382 >        
383 >    // excluded interaction, so just return
384 >    if (idat.excluded) return;
385  
386 <    switcher_->setSwitchType(sft_);
458 <    switcher_->setSwitch(rSwitch_, rCut_);
459 <  }
386 >    int& iHash = iHash_[idat.atid1][idat.atid2];
387  
388 <  /**
389 <   * 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() {  
388 >    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389 >    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);
390  
391 <    Globals* simParams_ = info_->getSimParams();    
470 <  
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 <    }            
391 >    // set<NonBondedInteraction*>::iterator it;
392  
393 <    listRadius_ = rCut_ + skinThickness_;
394 <  }
395 <
396 <
397 <  void InteractionManager::doPrePair(InteractionData idat){
393 >    // for (it = interactions_[ idat.atypes ].begin();
394 >    //      it != interactions_[ idat.atypes ].end(); ++it){
395 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
396 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
397 >    //   }
398 >    // }
399      
490 –    if (!initialized_) initialize();
491 –        
492 –    set<NonBondedInteraction*>::iterator it;
493 –
494 –    for (it = interactions_[ *(idat.atypes) ].begin();
495 –         it != interactions_[ *(idat.atypes) ].end(); ++it){
496 –      if ((*it)->getFamily() == METALLIC_FAMILY) {
497 –        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
498 –      }
499 –    }
500 –    
400      return;    
401    }
402    
403 <  void InteractionManager::doPreForce(SelfData sdat){
403 >  void InteractionManager::doPreForce(SelfData &sdat){
404  
405      if (!initialized_) initialize();
406      
407 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
408 <    set<NonBondedInteraction*>::iterator it;
407 >    int& iHash = iHash_[sdat.atid][sdat.atid];
408 >
409 >    if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
410 >    if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);
411 >
412 >    // set<NonBondedInteraction*>::iterator it;
413      
414 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
415 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
416 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417 <      }
418 <    }
414 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
415 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417 >    //   }
418 >    // }
419      
420      return;    
421    }
422  
423 <  void InteractionManager::doPair(InteractionData idat){
423 >  void InteractionManager::doPair(InteractionData &idat){
424      
425      if (!initialized_) initialize();
523 –  
524 –    set<NonBondedInteraction*>::iterator it;
426  
427 <    for (it = interactions_[ *(idat.atypes) ].begin();
527 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
528 <      (*it)->calcForce(idat);
529 <    
530 <    return;    
531 <  }
427 >    int& iHash = iHash_[idat.atid1][idat.atid2];
428  
429 <  void InteractionManager::doSkipCorrection(InteractionData idat){
429 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430 >      
431 >    // electrostatics still has to worry about indirect
432 >    // contributions from excluded pairs of atoms, but nothing else does:
433  
434 <    if (!initialized_) initialize();  
536 <    
537 <    set<NonBondedInteraction*>::iterator it;
434 >    if (idat.excluded) return;
435  
436 <    for (it = interactions_[ *(idat.atypes) ].begin();
437 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
438 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
439 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
440 <      }
441 <    }
436 >    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
437 >    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
438 >    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
439 >    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
440 >    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
441 >    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
442 >    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
443 >    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);
444 >
445 >    // set<NonBondedInteraction*>::iterator it;
446 >
447 >    // for (it = interactions_[ idat.atypes ].begin();
448 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
449 >
450 >    //   // electrostatics still has to worry about indirect
451 >    //   // contributions from excluded pairs of atoms:
452 >
453 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
454 >    //     (*it)->calcForce(idat);
455 >    //   }
456 >    // }
457      
458      return;    
459    }
460  
461 <  void InteractionManager::doSelfCorrection(SelfData sdat){
461 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
462  
463      if (!initialized_) initialize();
464      
465 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
554 <    set<NonBondedInteraction*>::iterator it;
465 >    int& iHash = iHash_[sdat.atid][sdat.atid];
466  
467 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
468 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
469 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
470 <      }
471 <    }
467 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468 >
469 >    // set<NonBondedInteraction*>::iterator it;
470 >
471 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
472 >    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 >    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
474 >    //   }
475 >    // }
476        
477      return;    
478    }
479  
480 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
481 +    if (!initialized_) initialize();
482 +    electrostatic_->ReciprocalSpaceSum(pot);
483 +  }
484 +
485    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
486      if (!initialized_) initialize();
487 <    
487 >
488      AtomType* atype = typeMap_[*atid];
489  
570 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
490      set<NonBondedInteraction*>::iterator it;
491      RealType cutoff = 0.0;
492      
493 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
494 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
493 >    for (it = interactions_[*atid][*atid].begin();
494 >         it != interactions_[*atid][*atid].end();
495 >         ++it)
496 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
497      return cutoff;    
498    }
499  
500    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
501      if (!initialized_) initialize();
502      
503 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
503 >    int atid = atype->getIdent();
504 >
505      set<NonBondedInteraction*>::iterator it;
506      RealType cutoff = 0.0;
507      
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
509 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
508 >    for (it = interactions_[atid][atid].begin();
509 >         it != interactions_[atid][atid].end(); ++it)
510 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
511      return cutoff;    
512    }
513   } //end namespace OpenMD

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