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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 2033 by gezelter, Sat Nov 1 14:12:16 2014 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 +    sHash_.resize(nTypes);
94 +    iHash_.resize(nTypes);
95 +    interactions_.resize(nTypes);
96      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
97      AtomType* atype1;
98      AtomType* atype2;
99 <    pair<AtomType*, AtomType*> key;
100 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
99 >    int atid1, atid2;
100 >
101 >    // We only need to worry about the types that are actually in the
102 >    // simulation:
103      
104 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
105 <         atype1 = atomTypes->nextType(i1)) {
106 <      
107 <      // add it to the map:
108 <      AtomTypeProperties atp = atype1->getATP();    
109 <      
104 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
105 >
106 >    lj_->setSimulatedAtomTypes(atypes);
107 >    gb_->setSimulatedAtomTypes(atypes);
108 >    sticky_->setSimulatedAtomTypes(atypes);
109 >    eam_->setSimulatedAtomTypes(atypes);
110 >    sc_->setSimulatedAtomTypes(atypes);
111 >    morse_->setSimulatedAtomTypes(atypes);
112 >    electrostatic_->setSimInfo(info_);
113 >    electrostatic_->setSimulatedAtomTypes(atypes);
114 >    maw_->setSimulatedAtomTypes(atypes);
115 >    repulsivePower_->setSimulatedAtomTypes(atypes);
116 >
117 >    set<AtomType*>::iterator at;
118 >
119 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
120 >          
121 >      atype1 = *at;
122 >      atid1 = atype1->getIdent();
123 >      iHash_[atid1].resize(nTypes);
124 >      interactions_[atid1].resize(nTypes);
125 >
126 >      // add it to the map:      
127        pair<map<int,AtomType*>::iterator,bool> ret;    
128 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
128 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
129        if (ret.second == false) {
130          sprintf( painCave.errMsg,
131                   "InteractionManager already had a previous entry with ident %d\n",
132 <                 atp.ident);
132 >                 atype1->getIdent());
133          painCave.severity = OPENMD_INFO;
134          painCave.isFatal = 0;
135          simError();                
136        }
137 +          
138 +      if (atype1->isLennardJones()) {
139 +        sHash_[atid1] |= LJ_INTERACTION;
140 +      }
141 +      if (atype1->isElectrostatic()) {
142 +        sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
143 +      }
144 +      if (atype1->isSticky()) {
145 +        sHash_[atid1] |= STICKY_INTERACTION;
146 +      }
147 +      if (atype1->isStickyPower()) {
148 +        sHash_[atid1] |= STICKY_INTERACTION;
149 +      }
150 +      if (atype1->isEAM()) {      
151 +        sHash_[atid1] |= EAM_INTERACTION;
152 +      }
153 +      if (atype1->isSC()) {
154 +        sHash_[atid1] |= SC_INTERACTION;
155 +      }
156 +      if (atype1->isGayBerne()) {
157 +        sHash_[atid1] |= GB_INTERACTION;
158 +      }
159      }
136 –    
160      // Now, iterate over all known types and add to the interaction map:
161      
162      map<int, AtomType*>::iterator it1, it2;
163      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
164        atype1 = (*it1).second;
165 +      atid1 = atype1->getIdent();
166  
167        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
168          atype2 = (*it2).second;
169 +        atid2 = atype2->getIdent();
170 +                              
171 +        iHash_[atid1][atid2] = 0;
172          
146 –        bool vdwExplicit = false;
147 –        bool metExplicit = false;
148 –        bool hbExplicit = false;
149 –                      
150 –        key = make_pair(atype1, atype2);
151 –        
173          if (atype1->isLennardJones() && atype2->isLennardJones()) {
174 <          interactions_[key].insert(lj_);
174 >          interactions_[atid1][atid2].insert(lj_);
175 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
176          }
177          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
178 <          interactions_[key].insert(electrostatic_);
178 >          interactions_[atid1][atid2].insert(electrostatic_);
179 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
180          }
181          if (atype1->isSticky() && atype2->isSticky() ) {
182 <          interactions_[key].insert(sticky_);
182 >          interactions_[atid1][atid2].insert(sticky_);
183 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
184          }
185          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
186 <          interactions_[key].insert(sticky_);
186 >          interactions_[atid1][atid2].insert(sticky_);
187 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
188          }
189          if (atype1->isEAM() && atype2->isEAM() ) {
190 <          interactions_[key].insert(eam_);
190 >          interactions_[atid1][atid2].insert(eam_);
191 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
192          }
193          if (atype1->isSC() && atype2->isSC() ) {
194 <          interactions_[key].insert(sc_);
194 >          interactions_[atid1][atid2].insert(sc_);
195 >          iHash_[atid1][atid2] |= SC_INTERACTION;
196          }
197          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
198 <          interactions_[key].insert(gb_);
198 >          interactions_[atid1][atid2].insert(gb_);
199 >          iHash_[atid1][atid2] |= GB_INTERACTION;
200          }
201          if ((atype1->isGayBerne() && atype2->isLennardJones())
202              || (atype1->isLennardJones() && atype2->isGayBerne())) {
203 <          interactions_[key].insert(gb_);
203 >          interactions_[atid1][atid2].insert(gb_);
204 >          iHash_[atid1][atid2] |= GB_INTERACTION;
205          }
206          
207          // look for an explicitly-set non-bonded interaction type using the
# Line 181 | Line 210 | namespace OpenMD {
210          
211          if (nbiType != NULL) {
212  
213 +          bool vdwExplicit = false;
214 +          bool metExplicit = false;
215 +          // bool hbExplicit = false;
216 +
217            if (nbiType->isLennardJones()) {
218              // We found an explicit Lennard-Jones interaction.  
219              // override all other vdw entries for this pair of atom types:
220              set<NonBondedInteraction*>::iterator it;
221 <            for (it = interactions_[key].begin();
222 <                 it != interactions_[key].end(); ++it) {
221 >            for (it = interactions_[atid1][atid2].begin();
222 >                 it != interactions_[atid1][atid2].end(); ++it) {
223                InteractionFamily ifam = (*it)->getFamily();
224 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
224 >              if (ifam == VANDERWAALS_FAMILY) {
225 >                interactions_[atid1][atid2].erase(*it);
226 >                iHash_[atid1][atid2] ^= (*it)->getHash();
227 >              }
228              }
229 <            interactions_[key].insert(lj_);
229 >            interactions_[atid1][atid2].insert(lj_);
230 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
231              vdwExplicit = true;
232            }
233            
# Line 208 | Line 245 | namespace OpenMD {
245              // We found an explicit Morse interaction.  
246              // override all other vdw entries for this pair of atom types:
247              set<NonBondedInteraction*>::iterator it;
248 <            for (it = interactions_[key].begin();
249 <                 it != interactions_[key].end(); ++it) {
248 >            for (it = interactions_[atid1][atid2].begin();
249 >                 it != interactions_[atid1][atid2].end(); ++it) {
250                InteractionFamily ifam = (*it)->getFamily();
251 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
251 >              if (ifam == VANDERWAALS_FAMILY) {
252 >                interactions_[atid1][atid2].erase(*it);
253 >                iHash_[atid1][atid2] ^= (*it)->getHash();
254 >              }
255              }
256 <            interactions_[key].insert(morse_);
256 >            interactions_[atid1][atid2].insert(morse_);
257 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
258              vdwExplicit = true;
259            }
260 +
261 +          if (nbiType->isRepulsivePower()) {
262 +            if (vdwExplicit) {
263 +              sprintf( painCave.errMsg,
264 +                       "InteractionManager::initialize found more than one "
265 +                       "explicit \n"
266 +                       "\tvan der Waals interaction for atom types %s - %s\n",
267 +                       atype1->getName().c_str(), atype2->getName().c_str());
268 +              painCave.severity = OPENMD_ERROR;
269 +              painCave.isFatal = 1;
270 +              simError();
271 +            }
272 +            // We found an explicit RepulsivePower interaction.  
273 +            // override all other vdw entries for this pair of atom types:
274 +            set<NonBondedInteraction*>::iterator it;
275 +            for (it = interactions_[atid1][atid2].begin();
276 +                 it != interactions_[atid1][atid2].end(); ++it) {
277 +              InteractionFamily ifam = (*it)->getFamily();
278 +              if (ifam == VANDERWAALS_FAMILY) {
279 +                interactions_[atid1][atid2].erase(*it);
280 +                iHash_[atid1][atid2] ^= (*it)->getHash();
281 +              }
282 +            }
283 +            interactions_[atid1][atid2].insert(repulsivePower_);
284 +            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
285 +            vdwExplicit = true;
286 +          }
287            
288 +          
289            if (nbiType->isEAM()) {
290              // We found an explicit EAM interaction.  
291              // override all other metallic entries for this pair of atom types:
292              set<NonBondedInteraction*>::iterator it;
293 <            for (it = interactions_[key].begin();
294 <                 it != interactions_[key].end(); ++it) {
293 >            for (it = interactions_[atid1][atid2].begin();
294 >                 it != interactions_[atid1][atid2].end(); ++it) {
295                InteractionFamily ifam = (*it)->getFamily();
296 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
296 >              if (ifam == METALLIC_FAMILY) {
297 >                interactions_[atid1][atid2].erase(*it);
298 >                iHash_[atid1][atid2] ^= (*it)->getHash();
299 >              }
300              }
301 <            interactions_[key].insert(eam_);
301 >            interactions_[atid1][atid2].insert(eam_);
302 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
303              metExplicit = true;
304            }
305            
# Line 244 | Line 317 | namespace OpenMD {
317              // We found an explicit Sutton-Chen interaction.  
318              // override all other metallic entries for this pair of atom types:
319              set<NonBondedInteraction*>::iterator it;
320 <            for (it = interactions_[key].begin();
321 <                 it != interactions_[key].end(); ++it) {
320 >            for (it = interactions_[atid1][atid2].begin();
321 >                 it != interactions_[atid1][atid2].end(); ++it) {
322                InteractionFamily ifam = (*it)->getFamily();
323 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
323 >              if (ifam == METALLIC_FAMILY) {
324 >                interactions_[atid1][atid2].erase(*it);
325 >                iHash_[atid1][atid2] ^= (*it)->getHash();
326 >              }
327              }
328 <            interactions_[key].insert(sc_);
328 >            interactions_[atid1][atid2].insert(sc_);
329 >            iHash_[atid1][atid2] |= SC_INTERACTION;
330              metExplicit = true;
331            }
332            
# Line 267 | Line 344 | namespace OpenMD {
344              // We found an explicit MAW interaction.  
345              // override all other vdw entries for this pair of atom types:
346              set<NonBondedInteraction*>::iterator it;
347 <            for (it = interactions_[key].begin();
348 <                 it != interactions_[key].end(); ++it) {
347 >            for (it = interactions_[atid1][atid2].begin();
348 >                 it != interactions_[atid1][atid2].end(); ++it) {
349                InteractionFamily ifam = (*it)->getFamily();
350 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
350 >              if (ifam == VANDERWAALS_FAMILY) {
351 >                interactions_[atid1][atid2].erase(*it);
352 >                iHash_[atid1][atid2] ^= (*it)->getHash();
353 >              }
354              }
355 <            interactions_[key].insert(maw_);
355 >            interactions_[atid1][atid2].insert(maw_);
356 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
357              vdwExplicit = true;
358            }        
359          }
# Line 280 | Line 361 | namespace OpenMD {
361      }
362      
363      
364 <    // make sure every pair of atom types in this simulation has a
365 <    // non-bonded interaction:
364 >    // Make sure every pair of atom types in this simulation has a
365 >    // non-bonded interaction.  If not, just inform the user.
366  
367      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
368      set<AtomType*>::iterator it, jt;
369 +
370      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
371        atype1 = (*it);
372 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
372 >      atid1 = atype1->getIdent();
373 >      for (jt = it; jt != simTypes.end(); ++jt) {
374          atype2 = (*jt);
375 <        key = make_pair(atype1, atype2);
375 >        atid2 = atype2->getIdent();
376          
377 <        if (interactions_[key].size() == 0) {
377 >        if (interactions_[atid1][atid2].size() == 0) {
378            sprintf( painCave.errMsg,
379 <                   "InteractionManager unable to find an appropriate non-bonded\n"
380 <                   "\tinteraction for atom types %s - %s\n",
379 >                   "InteractionManager could not find a matching non-bonded\n"
380 >                   "\tinteraction for atom types %s - %s\n"
381 >                   "\tProceeding without this interaction.\n",
382                     atype1->getName().c_str(), atype2->getName().c_str());
383            painCave.severity = OPENMD_INFO;
384 <          painCave.isFatal = 1;
384 >          painCave.isFatal = 0;
385            simError();
386          }
387        }
388      }
389  
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 –
390      initialized_ = true;
391    }
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 –    }
392  
393 <    map<string, CutoffMethod> stringToCutoffMethod;
394 <    stringToCutoffMethod["HARD"] = HARD;
395 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
396 <    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 <    }
393 >  void InteractionManager::setCutoffRadius(RealType rcut) {
394 >    
395 >    electrostatic_->setCutoffRadius(rcut);
396 >    eam_->setCutoffRadius(rcut);
397    }
398  
399 <
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 <    }          
399 >  void InteractionManager::doPrePair(InteractionData &idat){
400      
401 <    if (simParams_->haveSwitchingFunctionType()) {
402 <      string funcType = simParams_->getSwitchingFunctionType();
403 <      toUpper(funcType);
404 <      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 <    }
401 >    if (!initialized_) initialize();
402 >        
403 >    // excluded interaction, so just return
404 >    if (idat.excluded) return;
405  
406 <    switcher_->setSwitchType(sft_);
458 <    switcher_->setSwitch(rSwitch_, rCut_);
459 <  }
406 >    int& iHash = iHash_[idat.atid1][idat.atid2];
407  
408 <  /**
409 <   * 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() {  
408 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
409 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
410  
411 <    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 <    }            
411 >    // set<NonBondedInteraction*>::iterator it;
412  
413 <    listRadius_ = rCut_ + skinThickness_;
414 <  }
415 <
416 <
417 <  void InteractionManager::doPrePair(InteractionData idat){
413 >    // for (it = interactions_[ idat.atypes ].begin();
414 >    //      it != interactions_[ idat.atypes ].end(); ++it){
415 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
417 >    //   }
418 >    // }
419      
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 –    
420      return;    
421    }
422    
423 <  void InteractionManager::doPreForce(SelfData sdat){
423 >  void InteractionManager::doPreForce(SelfData &sdat){
424  
425      if (!initialized_) initialize();
426      
427 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
428 <    set<NonBondedInteraction*>::iterator it;
427 >    int& sHash = sHash_[sdat.atid];
428 >
429 >    if ((sHash & EAM_INTERACTION) != 0)  eam_->calcFunctional(sdat);
430 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
431 >
432 >    // set<NonBondedInteraction*>::iterator it;
433      
434 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
435 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
436 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
437 <      }
438 <    }
434 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
435 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
436 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
437 >    //   }
438 >    // }
439      
440      return;    
441    }
442  
443 <  void InteractionManager::doPair(InteractionData idat){
443 >  void InteractionManager::doPair(InteractionData &idat){
444      
445      if (!initialized_) initialize();
523 –  
524 –    set<NonBondedInteraction*>::iterator it;
446  
447 <    for (it = interactions_[idat.atypes].begin();
527 <         it != interactions_[idat.atypes].end(); ++it)
528 <      (*it)->calcForce(idat);
529 <    
530 <    return;    
531 <  }
447 >    int& iHash = iHash_[idat.atid1][idat.atid2];
448  
449 <  void InteractionManager::doSkipCorrection(InteractionData idat){
449 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
450 >      
451 >    // electrostatics still has to worry about indirect
452 >    // contributions from excluded pairs of atoms, but nothing else does:
453  
454 <    if (!initialized_) initialize();  
536 <    
537 <    set<NonBondedInteraction*>::iterator it;
454 >    if (idat.excluded) return;
455  
456 <    for (it = interactions_[idat.atypes].begin();
457 <         it != interactions_[idat.atypes].end(); ++it){
458 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
459 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
460 <      }
461 <    }
456 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
457 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
458 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
459 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
460 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
461 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
462 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
463 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
464 >
465 >    // set<NonBondedInteraction*>::iterator it;
466 >
467 >    // for (it = interactions_[ idat.atypes ].begin();
468 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
469 >
470 >    //   // electrostatics still has to worry about indirect
471 >    //   // contributions from excluded pairs of atoms:
472 >
473 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
474 >    //     (*it)->calcForce(idat);
475 >    //   }
476 >    // }
477      
478      return;    
479    }
480  
481 <  void InteractionManager::doSelfCorrection(SelfData sdat){
481 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
482  
483      if (!initialized_) initialize();
484      
485 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
554 <    set<NonBondedInteraction*>::iterator it;
485 >    int& sHash = sHash_[sdat.atid];
486  
487 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
488 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
489 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
490 <      }
491 <    }
487 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
488 >
489 >    // set<NonBondedInteraction*>::iterator it;
490 >
491 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
492 >    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
493 >    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
494 >    //   }
495 >    // }
496        
497      return;    
498    }
499  
500 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
501 +    if (!initialized_) initialize();
502 +    electrostatic_->ReciprocalSpaceSum(pot);
503 +  }
504 +
505    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
506      if (!initialized_) initialize();
507 <    
507 >
508      AtomType* atype = typeMap_[*atid];
509  
570 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
510      set<NonBondedInteraction*>::iterator it;
511      RealType cutoff = 0.0;
512      
513 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
514 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
513 >    for (it = interactions_[*atid][*atid].begin();
514 >         it != interactions_[*atid][*atid].end();
515 >         ++it)
516 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
517 >                                                                     atype)));
518      return cutoff;    
519    }
520  
521    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
522      if (!initialized_) initialize();
523      
524 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
524 >    int atid = atype->getIdent();
525 >
526      set<NonBondedInteraction*>::iterator it;
527      RealType cutoff = 0.0;
528      
529 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
530 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
529 >    for (it = interactions_[atid][atid].begin();
530 >         it != interactions_[atid][atid].end(); ++it)
531 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
532 >                                                                     atype)));
533      return cutoff;    
534    }
535   } //end namespace OpenMD

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