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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
trunk/src/nonbonded/InteractionManager.cpp (file contents), Revision 2005 by gezelter, Wed Jun 11 18:37:56 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 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
52 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
53 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
54 <  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();
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;
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 84 | 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  
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 –
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;
101 <    
102 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
103 <         atype1 = atomTypes->nextType(i1)) {
104 <      
105 <      // add it to the map:
106 <      AtomTypeProperties atp = atype1->getATP();    
107 <      
99 >    int atid1, atid2;
100 >
101 >    // We only need to worry about the types that are actually in the simulation:
102 >
103 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
104 >
105 >    lj_->setSimulatedAtomTypes(atypes);
106 >    gb_->setSimulatedAtomTypes(atypes);
107 >    sticky_->setSimulatedAtomTypes(atypes);
108 >    eam_->setSimulatedAtomTypes(atypes);
109 >    sc_->setSimulatedAtomTypes(atypes);
110 >    morse_->setSimulatedAtomTypes(atypes);
111 >    electrostatic_->setSimInfo(info_);
112 >    electrostatic_->setSimulatedAtomTypes(atypes);
113 >    maw_->setSimulatedAtomTypes(atypes);
114 >    repulsivePower_->setSimulatedAtomTypes(atypes);
115 >
116 >    set<AtomType*>::iterator at;
117 >
118 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
119 >          
120 >      atype1 = *at;
121 >      atid1 = atype1->getIdent();
122 >      iHash_[atid1].resize(nTypes);
123 >      interactions_[atid1].resize(nTypes);
124 >
125 >      // add it to the map:      
126        pair<map<int,AtomType*>::iterator,bool> ret;    
127 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
127 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
128        if (ret.second == false) {
129          sprintf( painCave.errMsg,
130                   "InteractionManager already had a previous entry with ident %d\n",
131 <                 atp.ident);
131 >                 atype1->getIdent());
132          painCave.severity = OPENMD_INFO;
133          painCave.isFatal = 0;
134          simError();                
135        }
136 +          
137 +      if (atype1->isLennardJones()) {
138 +        sHash_[atid1] |= LJ_INTERACTION;
139 +      }
140 +      if (atype1->isElectrostatic()) {
141 +        sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
142 +      }
143 +      if (atype1->isSticky()) {
144 +        sHash_[atid1] |= STICKY_INTERACTION;
145 +      }
146 +      if (atype1->isStickyPower()) {
147 +        sHash_[atid1] |= STICKY_INTERACTION;
148 +      }
149 +      if (atype1->isEAM()) {      
150 +        sHash_[atid1] |= EAM_INTERACTION;
151 +      }
152 +      if (atype1->isSC()) {
153 +        sHash_[atid1] |= SC_INTERACTION;
154 +      }
155 +      if (atype1->isGayBerne()) {
156 +        sHash_[atid1] |= GB_INTERACTION;
157 +      }
158      }
134 –    
159      // Now, iterate over all known types and add to the interaction map:
160      
161      map<int, AtomType*>::iterator it1, it2;
162      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
163        atype1 = (*it1).second;
164 +      atid1 = atype1->getIdent();
165  
166        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
167          atype2 = (*it2).second;
168 +        atid2 = atype2->getIdent();
169 +                              
170 +        iHash_[atid1][atid2] = 0;
171          
144 –        bool vdwExplicit = false;
145 –        bool metExplicit = false;
146 –        bool hbExplicit = false;
147 –                      
148 –        key = make_pair(atype1, atype2);
149 –        
172          if (atype1->isLennardJones() && atype2->isLennardJones()) {
173 <          interactions_[key].insert(lj_);
173 >          interactions_[atid1][atid2].insert(lj_);
174 >          iHash_[atid1][atid2] |= LJ_INTERACTION;
175          }
176          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
177 <          interactions_[key].insert(electrostatic_);
177 >          interactions_[atid1][atid2].insert(electrostatic_);
178 >          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
179          }
180          if (atype1->isSticky() && atype2->isSticky() ) {
181 <          interactions_[key].insert(sticky_);
181 >          interactions_[atid1][atid2].insert(sticky_);
182 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
183          }
184          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
185 <          interactions_[key].insert(sticky_);
185 >          interactions_[atid1][atid2].insert(sticky_);
186 >          iHash_[atid1][atid2] |= STICKY_INTERACTION;
187          }
188          if (atype1->isEAM() && atype2->isEAM() ) {
189 <          interactions_[key].insert(eam_);
189 >          interactions_[atid1][atid2].insert(eam_);
190 >          iHash_[atid1][atid2] |= EAM_INTERACTION;
191          }
192          if (atype1->isSC() && atype2->isSC() ) {
193 <          interactions_[key].insert(sc_);
193 >          interactions_[atid1][atid2].insert(sc_);
194 >          iHash_[atid1][atid2] |= SC_INTERACTION;
195          }
196          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
197 <          interactions_[key].insert(gb_);
197 >          interactions_[atid1][atid2].insert(gb_);
198 >          iHash_[atid1][atid2] |= GB_INTERACTION;
199          }
200          if ((atype1->isGayBerne() && atype2->isLennardJones())
201              || (atype1->isLennardJones() && atype2->isGayBerne())) {
202 <          interactions_[key].insert(gb_);
202 >          interactions_[atid1][atid2].insert(gb_);
203 >          iHash_[atid1][atid2] |= GB_INTERACTION;
204          }
205          
206          // look for an explicitly-set non-bonded interaction type using the
# Line 179 | Line 209 | namespace OpenMD {
209          
210          if (nbiType != NULL) {
211  
212 +          bool vdwExplicit = false;
213 +          bool metExplicit = false;
214 +          // bool hbExplicit = false;
215 +
216            if (nbiType->isLennardJones()) {
217              // We found an explicit Lennard-Jones interaction.  
218              // override all other vdw entries for this pair of atom types:
219              set<NonBondedInteraction*>::iterator it;
220 <            for (it = interactions_[key].begin();
221 <                 it != interactions_[key].end(); ++it) {
220 >            for (it = interactions_[atid1][atid2].begin();
221 >                 it != interactions_[atid1][atid2].end(); ++it) {
222                InteractionFamily ifam = (*it)->getFamily();
223 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
223 >              if (ifam == VANDERWAALS_FAMILY) {
224 >                interactions_[atid1][atid2].erase(*it);
225 >                iHash_[atid1][atid2] ^= (*it)->getHash();
226 >              }
227              }
228 <            interactions_[key].insert(lj_);
228 >            interactions_[atid1][atid2].insert(lj_);
229 >            iHash_[atid1][atid2] |= LJ_INTERACTION;
230              vdwExplicit = true;
231            }
232            
# Line 206 | Line 244 | namespace OpenMD {
244              // We found an explicit Morse interaction.  
245              // override all other vdw entries for this pair of atom types:
246              set<NonBondedInteraction*>::iterator it;
247 <            for (it = interactions_[key].begin();
248 <                 it != interactions_[key].end(); ++it) {
247 >            for (it = interactions_[atid1][atid2].begin();
248 >                 it != interactions_[atid1][atid2].end(); ++it) {
249                InteractionFamily ifam = (*it)->getFamily();
250 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
250 >              if (ifam == VANDERWAALS_FAMILY) {
251 >                interactions_[atid1][atid2].erase(*it);
252 >                iHash_[atid1][atid2] ^= (*it)->getHash();
253 >              }
254              }
255 <            interactions_[key].insert(morse_);
255 >            interactions_[atid1][atid2].insert(morse_);
256 >            iHash_[atid1][atid2] |= MORSE_INTERACTION;
257              vdwExplicit = true;
258            }
259 +
260 +          if (nbiType->isRepulsivePower()) {
261 +            if (vdwExplicit) {
262 +              sprintf( painCave.errMsg,
263 +                       "InteractionManager::initialize found more than one "
264 +                       "explicit \n"
265 +                       "\tvan der Waals interaction for atom types %s - %s\n",
266 +                       atype1->getName().c_str(), atype2->getName().c_str());
267 +              painCave.severity = OPENMD_ERROR;
268 +              painCave.isFatal = 1;
269 +              simError();
270 +            }
271 +            // We found an explicit RepulsivePower interaction.  
272 +            // override all other vdw entries for this pair of atom types:
273 +            set<NonBondedInteraction*>::iterator it;
274 +            for (it = interactions_[atid1][atid2].begin();
275 +                 it != interactions_[atid1][atid2].end(); ++it) {
276 +              InteractionFamily ifam = (*it)->getFamily();
277 +              if (ifam == VANDERWAALS_FAMILY) {
278 +                interactions_[atid1][atid2].erase(*it);
279 +                iHash_[atid1][atid2] ^= (*it)->getHash();
280 +              }
281 +            }
282 +            interactions_[atid1][atid2].insert(repulsivePower_);
283 +            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
284 +            vdwExplicit = true;
285 +          }
286            
287 +          
288            if (nbiType->isEAM()) {
289              // We found an explicit EAM interaction.  
290              // override all other metallic entries for this pair of atom types:
291              set<NonBondedInteraction*>::iterator it;
292 <            for (it = interactions_[key].begin();
293 <                 it != interactions_[key].end(); ++it) {
292 >            for (it = interactions_[atid1][atid2].begin();
293 >                 it != interactions_[atid1][atid2].end(); ++it) {
294                InteractionFamily ifam = (*it)->getFamily();
295 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
295 >              if (ifam == METALLIC_FAMILY) {
296 >                interactions_[atid1][atid2].erase(*it);
297 >                iHash_[atid1][atid2] ^= (*it)->getHash();
298 >              }
299              }
300 <            interactions_[key].insert(eam_);
300 >            interactions_[atid1][atid2].insert(eam_);
301 >            iHash_[atid1][atid2] |= EAM_INTERACTION;
302              metExplicit = true;
303            }
304            
# Line 242 | Line 316 | namespace OpenMD {
316              // We found an explicit Sutton-Chen interaction.  
317              // override all other metallic entries for this pair of atom types:
318              set<NonBondedInteraction*>::iterator it;
319 <            for (it = interactions_[key].begin();
320 <                 it != interactions_[key].end(); ++it) {
319 >            for (it = interactions_[atid1][atid2].begin();
320 >                 it != interactions_[atid1][atid2].end(); ++it) {
321                InteractionFamily ifam = (*it)->getFamily();
322 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
322 >              if (ifam == METALLIC_FAMILY) {
323 >                interactions_[atid1][atid2].erase(*it);
324 >                iHash_[atid1][atid2] ^= (*it)->getHash();
325 >              }
326              }
327 <            interactions_[key].insert(sc_);
327 >            interactions_[atid1][atid2].insert(sc_);
328 >            iHash_[atid1][atid2] |= SC_INTERACTION;
329              metExplicit = true;
330            }
331            
# Line 265 | Line 343 | namespace OpenMD {
343              // We found an explicit MAW interaction.  
344              // override all other vdw entries for this pair of atom types:
345              set<NonBondedInteraction*>::iterator it;
346 <            for (it = interactions_[key].begin();
347 <                 it != interactions_[key].end(); ++it) {
346 >            for (it = interactions_[atid1][atid2].begin();
347 >                 it != interactions_[atid1][atid2].end(); ++it) {
348                InteractionFamily ifam = (*it)->getFamily();
349 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
349 >              if (ifam == VANDERWAALS_FAMILY) {
350 >                interactions_[atid1][atid2].erase(*it);
351 >                iHash_[atid1][atid2] ^= (*it)->getHash();
352 >              }
353              }
354 <            interactions_[key].insert(maw_);
354 >            interactions_[atid1][atid2].insert(maw_);
355 >            iHash_[atid1][atid2] |= MAW_INTERACTION;
356              vdwExplicit = true;
357            }        
358          }
# Line 278 | Line 360 | namespace OpenMD {
360      }
361      
362      
363 <    // make sure every pair of atom types in this simulation has a
364 <    // non-bonded interaction:
363 >    // Make sure every pair of atom types in this simulation has a
364 >    // non-bonded interaction.  If not, just inform the user.
365  
366      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
367      set<AtomType*>::iterator it, jt;
368 +
369      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
370        atype1 = (*it);
371 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
371 >      atid1 = atype1->getIdent();
372 >      for (jt = it; jt != simTypes.end(); ++jt) {
373          atype2 = (*jt);
374 <        key = make_pair(atype1, atype2);
374 >        atid2 = atype2->getIdent();
375          
376 <        if (interactions_[key].size() == 0) {
376 >        if (interactions_[atid1][atid2].size() == 0) {
377            sprintf( painCave.errMsg,
378 <                   "InteractionManager unable to find an appropriate non-bonded\n"
379 <                   "\tinteraction for atom types %s - %s\n",
378 >                   "InteractionManager could not find a matching non-bonded\n"
379 >                   "\tinteraction for atom types %s - %s\n"
380 >                   "\tProceeding without this interaction.\n",
381                     atype1->getName().c_str(), atype2->getName().c_str());
382            painCave.severity = OPENMD_INFO;
383 <          painCave.isFatal = 1;
383 >          painCave.isFatal = 0;
384            simError();
385          }
386        }
387      }
388  
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 –
389      initialized_ = true;
390    }
313 –  
314 –  /**
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() {
332 –    
333 –    Globals* simParams_ = info_->getSimParams();
334 –    
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 –    }
391  
392 <    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 <    }
397 <  }
398 <
399 <
400 <  /**
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 <    }          
392 >  void InteractionManager::setCutoffRadius(RealType rcut) {
393      
394 <    if (simParams_->haveSwitchingFunctionType()) {
395 <      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_);
394 >    electrostatic_->setCutoffRadius(rcut);
395 >    eam_->setCutoffRadius(rcut);
396    }
397  
398 <  void InteractionManager::doPrePair(InteractionData idat){
398 >  void InteractionManager::doPrePair(InteractionData &idat){
399      
400      if (!initialized_) initialize();
401          
402 <    set<NonBondedInteraction*>::iterator it;
402 >    // excluded interaction, so just return
403 >    if (idat.excluded) return;
404  
405 <    for (it = interactions_[ *(idat.atypes) ].begin();
406 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
407 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
408 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
409 <      }
410 <    }
405 >    int& iHash = iHash_[idat.atid1][idat.atid2];
406 >
407 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
408 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
409 >
410 >    // set<NonBondedInteraction*>::iterator it;
411 >
412 >    // for (it = interactions_[ idat.atypes ].begin();
413 >    //      it != interactions_[ idat.atypes ].end(); ++it){
414 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
415 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
416 >    //   }
417 >    // }
418      
419      return;    
420    }
421    
422 <  void InteractionManager::doPreForce(SelfData sdat){
422 >  void InteractionManager::doPreForce(SelfData &sdat){
423  
424      if (!initialized_) initialize();
425      
426 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
427 <    set<NonBondedInteraction*>::iterator it;
426 >    int& sHash = sHash_[sdat.atid];
427 >
428 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
429 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
430 >
431 >    // set<NonBondedInteraction*>::iterator it;
432      
433 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
434 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
435 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
436 <      }
437 <    }
433 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
434 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
435 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
436 >    //   }
437 >    // }
438      
439      return;    
440    }
441  
442 <  void InteractionManager::doPair(InteractionData idat){
442 >  void InteractionManager::doPair(InteractionData &idat){
443      
444      if (!initialized_) initialize();
492 –  
493 –    set<NonBondedInteraction*>::iterator it;
445  
446 <    for (it = interactions_[ *(idat.atypes) ].begin();
496 <         it != interactions_[ *(idat.atypes) ].end(); ++it)
497 <      (*it)->calcForce(idat);
498 <    
499 <    return;    
500 <  }
446 >    int& iHash = iHash_[idat.atid1][idat.atid2];
447  
448 <  void InteractionManager::doSkipCorrection(InteractionData idat){
448 >    if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
449 >      
450 >    // electrostatics still has to worry about indirect
451 >    // contributions from excluded pairs of atoms, but nothing else does:
452  
453 <    if (!initialized_) initialize();  
505 <    
506 <    set<NonBondedInteraction*>::iterator it;
453 >    if (idat.excluded) return;
454  
455 <    for (it = interactions_[ *(idat.atypes) ].begin();
456 <         it != interactions_[ *(idat.atypes) ].end(); ++it){
457 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
458 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
459 <      }
460 <    }
455 >    if ((iHash & LJ_INTERACTION) != 0)             lj_->calcForce(idat);
456 >    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
457 >    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
458 >    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
459 >    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
460 >    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
461 >    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
462 >    if ((iHash & MAW_INTERACTION) != 0)            maw_->calcForce(idat);
463 >
464 >    // set<NonBondedInteraction*>::iterator it;
465 >
466 >    // for (it = interactions_[ idat.atypes ].begin();
467 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
468 >
469 >    //   // electrostatics still has to worry about indirect
470 >    //   // contributions from excluded pairs of atoms:
471 >
472 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 >    //     (*it)->calcForce(idat);
474 >    //   }
475 >    // }
476      
477      return;    
478    }
479  
480 <  void InteractionManager::doSelfCorrection(SelfData sdat){
480 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
481  
482      if (!initialized_) initialize();
483      
484 <    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
523 <    set<NonBondedInteraction*>::iterator it;
484 >    int& sHash = sHash_[sdat.atid];
485  
486 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
487 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
488 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
489 <      }
490 <    }
486 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
487 >
488 >    // set<NonBondedInteraction*>::iterator it;
489 >
490 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
491 >    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
492 >    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
493 >    //   }
494 >    // }
495        
496      return;    
497    }
498  
499 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
500 +    if (!initialized_) initialize();
501 +    electrostatic_->ReciprocalSpaceSum(pot);
502 +  }
503 +
504    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
505      if (!initialized_) initialize();
506 <    
506 >
507      AtomType* atype = typeMap_[*atid];
508  
539 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
509      set<NonBondedInteraction*>::iterator it;
510      RealType cutoff = 0.0;
511      
512 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
513 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
512 >    for (it = interactions_[*atid][*atid].begin();
513 >         it != interactions_[*atid][*atid].end();
514 >         ++it)
515 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
516      return cutoff;    
517    }
518  
519    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
520      if (!initialized_) initialize();
521      
522 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
522 >    int atid = atype->getIdent();
523 >
524      set<NonBondedInteraction*>::iterator it;
525      RealType cutoff = 0.0;
526      
527 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
528 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
527 >    for (it = interactions_[atid][atid].begin();
528 >         it != interactions_[atid][atid].end(); ++it)
529 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
530      return cutoff;    
531    }
532   } //end namespace OpenMD

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