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root/OpenMD/trunk/src/nonbonded/InteractionManager.cpp
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branches/development/src/nonbonded/InteractionManager.cpp (file contents), Revision 1536 by gezelter, Wed Jan 5 14:49:05 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"
43 – #include "UseTheForce/doForces_interface.h"
44  
45   namespace OpenMD {
46  
47 <  InteractionManager* InteractionManager::_instance = NULL;
48 <  SimInfo* InteractionManager::info_ = NULL;
49 <  bool InteractionManager::initialized_ = false;
47 >  InteractionManager::InteractionManager() {
48  
49 <  RealType InteractionManager::rCut_ = 0.0;
50 <  RealType InteractionManager::rSwitch_ = 0.0;
51 <  RealType InteractionManager::skinThickness_ = 0.0;
52 <  RealType InteractionManager::listRadius_ = 0.0;
53 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
54 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
55 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
56 <  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
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();
70 <  MAW* InteractionManager::maw_ = new MAW();
71 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
72 <
73 <  InteractionManager* InteractionManager::Instance() {
74 <    if (!_instance) {
75 <      _instance = new InteractionManager();
76 <    }
77 <    return _instance;
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 87 | 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  
93 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
94 –
95 –    // Force fields can set options on how to scale van der Waals and electrostatic
96 –    // interactions for atoms connected via bonds, bends and torsions
97 –    // in this case the topological distance between atoms is:
98 –    // 0 = topologically unconnected
99 –    // 1 = bonded together
100 –    // 2 = connected via a bend
101 –    // 3 = connected via a torsion
102 –
103 –    vdwScale_[0] = 1.0;
104 –    vdwScale_[1] = fopts.getvdw12scale();
105 –    vdwScale_[2] = fopts.getvdw13scale();
106 –    vdwScale_[3] = fopts.getvdw14scale();
107 –
108 –    electrostaticScale_[0] = 1.0;
109 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
110 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112 –
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      }
137 –    
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          
147 –        bool vdwExplicit = false;
148 –        bool metExplicit = false;
149 –        bool hbExplicit = false;
150 –                      
151 –        key = make_pair(atype1, atype2);
152 –        
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 182 | 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 209 | 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 245 | 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 268 | 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 281 | 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  
307 –    setupCutoffs();
308 –    setupSwitching();
309 –    setupNeighborlists();
310 –
311 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
312 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
313 –    notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
314 –    notifyFortranSkinThickness(&skinThickness_);
315 –
389      initialized_ = true;
390    }
318 –  
319 –  /**
320 –   * setupCutoffs
321 –   *
322 –   * Sets the values of cutoffRadius and cutoffMethod
323 –   *
324 –   * cutoffRadius : realType
325 –   *  If the cutoffRadius was explicitly set, use that value.
326 –   *  If the cutoffRadius was not explicitly set:
327 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
328 –   *      No electrostatic atoms?  Poll the atom types present in the
329 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
330 –   *      Use the maximum suggested value that was found.
331 –   *
332 –   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
333 –   *      If cutoffMethod was explicitly set, use that choice.
334 –   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
335 –   */
336 –  void InteractionManager::setupCutoffs() {
337 –    
338 –    Globals* simParams_ = info_->getSimParams();
339 –    
340 –    if (simParams_->haveCutoffRadius()) {
341 –      rCut_ = simParams_->getCutoffRadius();
342 –    } else {      
343 –      if (info_->usesElectrostaticAtoms()) {
344 –        sprintf(painCave.errMsg,
345 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
346 –                "\tOpenMD will use a default value of 12.0 angstroms"
347 –                "\tfor the cutoffRadius.\n");
348 –        painCave.isFatal = 0;
349 –        painCave.severity = OPENMD_INFO;
350 –        simError();
351 –        rCut_ = 12.0;
352 –      } else {
353 –        RealType thisCut;
354 –        set<AtomType*>::iterator i;
355 –        set<AtomType*> atomTypes;
356 –        atomTypes = info_->getSimulatedAtomTypes();        
357 –        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
358 –          thisCut = getSuggestedCutoffRadius((*i));
359 –          rCut_ = max(thisCut, rCut_);
360 –        }
361 –        sprintf(painCave.errMsg,
362 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
363 –                "\tOpenMD will use %lf angstroms.\n",
364 –                rCut_);
365 –        painCave.isFatal = 0;
366 –        painCave.severity = OPENMD_INFO;
367 –        simError();
368 –      }            
369 –    }
391  
392 <    map<string, CutoffMethod> stringToCutoffMethod;
372 <    stringToCutoffMethod["HARD"] = HARD;
373 <    stringToCutoffMethod["SWITCHED"] = SWITCHED;
374 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
375 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
376 <  
377 <    if (simParams_->haveCutoffMethod()) {
378 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
379 <      map<string, CutoffMethod>::iterator i;
380 <      i = stringToCutoffMethod.find(cutMeth);
381 <      if (i == stringToCutoffMethod.end()) {
382 <        sprintf(painCave.errMsg,
383 <                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
384 <                "\tShould be one of: "
385 <                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
386 <                cutMeth.c_str());
387 <        painCave.isFatal = 1;
388 <        painCave.severity = OPENMD_ERROR;
389 <        simError();
390 <      } else {
391 <        cutoffMethod_ = i->second;
392 <      }
393 <    } else {
394 <      sprintf(painCave.errMsg,
395 <              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
396 <              "\tOpenMD will use SHIFTED_FORCE.\n");
397 <        painCave.isFatal = 0;
398 <        painCave.severity = OPENMD_INFO;
399 <        simError();
400 <        cutoffMethod_ = SHIFTED_FORCE;        
401 <    }
402 <  }
403 <
404 <
405 <  /**
406 <   * setupSwitching
407 <   *
408 <   * Sets the values of switchingRadius and
409 <   *  If the switchingRadius was explicitly set, use that value (but check it)
410 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
411 <   */
412 <  void InteractionManager::setupSwitching() {
413 <    Globals* simParams_ = info_->getSimParams();
414 <
415 <    if (simParams_->haveSwitchingRadius()) {
416 <      rSwitch_ = simParams_->getSwitchingRadius();
417 <      if (rSwitch_ > rCut_) {        
418 <        sprintf(painCave.errMsg,
419 <                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
420 <                rSwitch_, rCut_);
421 <        painCave.isFatal = 1;
422 <        painCave.severity = OPENMD_ERROR;
423 <        simError();
424 <      }
425 <    } else {      
426 <      rSwitch_ = 0.85 * rCut_;
427 <      sprintf(painCave.errMsg,
428 <              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
429 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
430 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
431 <      painCave.isFatal = 0;
432 <      painCave.severity = OPENMD_WARNING;
433 <      simError();
434 <    }          
392 >  void InteractionManager::setCutoffRadius(RealType rcut) {
393      
394 <    if (simParams_->haveSwitchingFunctionType()) {
395 <      string funcType = simParams_->getSwitchingFunctionType();
438 <      toUpper(funcType);
439 <      if (funcType == "CUBIC") {
440 <        sft_ = cubic;
441 <      } else {
442 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
443 <          sft_ = fifth_order_poly;
444 <        } else {
445 <          // throw error        
446 <          sprintf( painCave.errMsg,
447 <                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
448 <                   "\tswitchingFunctionType must be one of: "
449 <                   "\"cubic\" or \"fifth_order_polynomial\".",
450 <                   funcType.c_str() );
451 <          painCave.isFatal = 1;
452 <          painCave.severity = OPENMD_ERROR;
453 <          simError();
454 <        }          
455 <      }
456 <    }
457 <
458 <    switcher_->setSwitchType(sft_);
459 <    switcher_->setSwitch(rSwitch_, rCut_);
394 >    electrostatic_->setCutoffRadius(rcut);
395 >    eam_->setCutoffRadius(rcut);
396    }
397  
398 <  /**
463 <   * setupNeighborlists
464 <   *
465 <   *  If the skinThickness was explicitly set, use that value (but check it)
466 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
467 <   */
468 <  void InteractionManager::setupNeighborlists() {  
469 <
470 <    Globals* simParams_ = info_->getSimParams();    
471 <  
472 <    if (simParams_->haveSkinThickness()) {
473 <      skinThickness_ = simParams_->getSkinThickness();
474 <    } else {      
475 <      skinThickness_ = 1.0;
476 <      sprintf(painCave.errMsg,
477 <              "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n"
478 <              "\tOpenMD will use a default value of %f Angstroms\n"
479 <              "\tfor this simulation\n", skinThickness_);
480 <      painCave.severity = OPENMD_INFO;
481 <      painCave.isFatal = 0;
482 <      simError();
483 <    }            
484 <
485 <    listRadius_ = rCut_ + skinThickness_;
486 <  }
487 <
488 <
489 <  void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
398 >  void InteractionManager::doPrePair(InteractionData &idat){
399      
400      if (!initialized_) initialize();
401 <          
402 <    DensityData ddat;
401 >        
402 >    // excluded interaction, so just return
403 >    if (idat.excluded) return;
404  
405 <    ddat.atype1 = typeMap_[*atid1];
496 <    ddat.atype2 = typeMap_[*atid2];
497 <    ddat.rij = *rij;
498 <    ddat.rho_i_at_j = *rho_i_at_j;
499 <    ddat.rho_j_at_i = *rho_j_at_i;
405 >    int& iHash = iHash_[idat.atid1][idat.atid2];
406  
407 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
408 <    set<NonBondedInteraction*>::iterator it;
407 >    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
408 >    if ((iHash & SC_INTERACTION) != 0)  sc_->calcDensity(idat);
409  
410 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
411 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
412 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
413 <      }
414 <    }
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(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
422 >  void InteractionManager::doPreForce(SelfData &sdat){
423  
424      if (!initialized_) initialize();
425 <          
426 <    FunctionalData fdat;
425 >    
426 >    int& sHash = sHash_[sdat.atid];
427  
428 <    fdat.atype = typeMap_[*atid];
429 <    fdat.rho = *rho;
521 <    fdat.frho = *frho;
522 <    fdat.dfrhodrho = *dfrhodrho;
428 >    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
429 >    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);
430  
431 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
525 <    set<NonBondedInteraction*>::iterator it;
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(fdat);
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(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *sw, int *topoDist, RealType *A1, RealType *A2, RealType *eFrame1, RealType *eFrame2, RealType *vpair, RealType *pot, RealType  *f1, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){
442 >  void InteractionManager::doPair(InteractionData &idat){
443      
444      if (!initialized_) initialize();
539 –    
540 –    InteractionData idat;
541 –    
542 –    idat.atype1 = typeMap_[*atid1];
543 –    idat.atype2 = typeMap_[*atid2];
544 –    idat.d = Vector3d(d);
545 –    idat.rij = *r;
546 –    idat.r2 = *r2;
547 –    idat.sw = *sw;
548 –    idat.vdwMult = vdwScale_[*topoDist];
549 –    idat.electroMult = electrostaticScale_[*topoDist];
550 –    for (int i = 0; i < 4; i++) {
551 –      idat.vpair[i] = vpair[i];
552 –      idat.pot[i] = pot[i];
553 –    }
554 –    idat.f1 = Vector3d(f1[0], f1[1], f1[2]);
555 –    idat.eFrame1 = Mat3x3d(eFrame1);
556 –    idat.eFrame2 = Mat3x3d(eFrame2);
557 –    idat.A1 = RotMat3x3d(A1);
558 –    idat.A2 = RotMat3x3d(A2);
559 –    idat.t1 = Vector3d(t1);
560 –    idat.t2 = Vector3d(t2);
561 –    idat.rho1 = *rho1;
562 –    idat.rho2 = *rho2;
563 –    idat.dfrho1 = *dfrho1;
564 –    idat.dfrho2 = *dfrho2;
565 –    idat.fshift1 = *fshift1;
566 –    idat.fshift2 = *fshift2;
445  
446 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
569 <    set<NonBondedInteraction*>::iterator it;
446 >    int& iHash = iHash_[idat.atid1][idat.atid2];
447  
448 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
449 <      (*it)->calcForce(idat);
450 <    
451 <    for (int i = 0; i < 4; i++) {
575 <      vpair[i] = idat.vpair[i];
576 <      pot[i] = idat.pot[i];
577 <    }
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 <    for (int i = 0; i < 3; i++) {
580 <      f1[i] = idat.f1[i];
581 <      t1[i] = idat.t1[i];
582 <      t2[i] = idat.t2[i];
583 <    }
453 >    if (idat.excluded) return;
454  
455 <    return;    
456 <  }
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 <  void InteractionManager::doSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){
464 >    // set<NonBondedInteraction*>::iterator it;
465  
466 <    if (!initialized_) initialize();
467 <    
592 <    SkipCorrectionData skdat;
593 <    
594 <    skdat.atype1 = typeMap_[*atid1];
595 <    skdat.atype2 = typeMap_[*atid2];
596 <    skdat.d = Vector3d(d);
597 <    skdat.rij = *r;
598 <    skdat.skippedCharge1 = *skippedCharge1;
599 <    skdat.skippedCharge2 = *skippedCharge2;
600 <    skdat.sw = *sw;
601 <    skdat.electroMult = *electroMult;
602 <    for (int i = 0; i < 4; i++) {
603 <      skdat.vpair[i] = vpair[i];
604 <      skdat.pot[i] = pot[i];
605 <    }
606 <    skdat.f1 = Vector3d(f1);
607 <    skdat.eFrame1 = Mat3x3d(eFrame1);
608 <    skdat.eFrame2 = Mat3x3d(eFrame2);
609 <    skdat.t1 = Vector3d(t1);
610 <    skdat.t2 = Vector3d(t2);
466 >    // for (it = interactions_[ idat.atypes ].begin();
467 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
468  
469 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
470 <    set<NonBondedInteraction*>::iterator it;
469 >    //   // electrostatics still has to worry about indirect
470 >    //   // contributions from excluded pairs of atoms:
471  
472 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
473 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
474 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
475 <      }
619 <    }
472 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 >    //     (*it)->calcForce(idat);
474 >    //   }
475 >    // }
476      
621 –    for (int i = 0; i < 4; i++) {
622 –      vpair[i] = skdat.vpair[i];
623 –      pot[i] = skdat.pot[i];
624 –    }
625 –
626 –    for (int i = 0; i < 3; i++) {
627 –      f1[i] = skdat.f1[i];
628 –      t1[i] = skdat.t1[i];
629 –      t2[i] = skdat.t2[i];
630 –    }
631 –
477      return;    
478    }
479  
480 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
480 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
481  
482      if (!initialized_) initialize();
483      
484 <    SelfCorrectionData scdat;
640 <    
641 <    scdat.atype = typeMap_[*atid];
642 <    scdat.eFrame = Mat3x3d(eFrame);
643 <    scdat.skippedCharge = *skippedCharge;
644 <    for (int i = 0; i < 4; i++){
645 <      scdat.pot[i] = pot[i];
646 <    }    
647 <    scdat.t = Vector3d(t);
484 >    int& sHash = sHash_[sdat.atid];
485  
486 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
650 <    set<NonBondedInteraction*>::iterator it;
486 >    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
487  
488 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
653 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
654 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
655 <      }
656 <    }
657 <      
658 <    t[0] = scdat.t.x();
659 <    t[1] = scdat.t.y();
660 <    t[2] = scdat.t.z();
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  
671 –    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(atype, atype));  
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(atype, atype));  
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    }
691 –
692 –  void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
693 –                                     int *in_switching_region) {
694 –    bool isr = switcher_->getSwitch( *r2 , *sw, *dswdr, *r);    
695 –    *in_switching_region = (int)isr;
696 –  }
697 –
532   } //end namespace OpenMD
699 –
700 – extern "C" {
701 –  
702 – #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
703 – #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
704 – #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
705 – #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
706 – #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
707 – #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
708 – #define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH)
709 –
710 –  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
711 –                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
712 –            
713 –    return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij,
714 –                                                             rho_i_at_j,  
715 –                                                             rho_j_at_i);
716 –  }
717 –  void fortranDoPreForce(int *atid, RealType *rho, RealType *frho,
718 –                         RealType *dfrhodrho) {  
719 –    
720 –    return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho,
721 –                                                              dfrhodrho);    
722 –  }
723 –  
724 –  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2,
725 –                     RealType *sw, int *topoDist, RealType *A1, RealType *A2,
726 –                     RealType *eFrame1, RealType *eFrame2,
727 –                     RealType *vpair, RealType *pot,
728 –                     RealType *f1, RealType *t1, RealType *t2,
729 –                     RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2,
730 –                     RealType *fshift1, RealType *fshift2){
731 –    
732 –    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r, r2,
733 –                                                          sw, topoDist, A1, A2,
734 –                                                          eFrame1, eFrame2,
735 –                                                          vpair, pot,
736 –                                                          f1, t1, t2,
737 –                                                          rho1, rho2,
738 –                                                          dfrho1, dfrho2,
739 –                                                          fshift1, fshift2);
740 –  }
741 –  
742 –  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d,
743 –                               RealType *r, RealType *skippedCharge1,
744 –                               RealType *skippedCharge2, RealType *sw,
745 –                               RealType *electroMult, RealType *pot,
746 –                               RealType *vpair, RealType *f1,
747 –                               RealType *eFrame1, RealType *eFrame2,
748 –                               RealType *t1, RealType *t2){
749 –    
750 –    return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1,
751 –                                                                    atid2, d,
752 –                                                                    r,
753 –                                                                    skippedCharge1,
754 –                                                                    skippedCharge2,
755 –                                                                    sw, electroMult, pot,
756 –                                                                    vpair, f1, eFrame1,
757 –                                                                    eFrame2, t1, t2);
758 –  }
759 –  
760 –  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
761 –                               RealType *pot, RealType *t) {
762 –    
763 –    return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid,
764 –                                                                    eFrame,
765 –                                                                    skippedCharge,
766 –                                                                    pot, t);
767 –  }
768 –  RealType fortranGetCutoff(int *atid) {    
769 –    return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid);
770 –  }
771 –
772 –  void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
773 –                        int *in_switching_region) {    
774 –    return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r,
775 –                                                             in_switching_region);
776 –  }  
777 – }

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