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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 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "nonbonded/InteractionManager.hpp"
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 +    iHash_.resize(nTypes);
94 +    interactions_.resize(nTypes);
95      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
96      AtomType* atype1;
97      AtomType* atype2;
98 <    pair<AtomType*, AtomType*> key;
99 <    pair<set<NonBondedInteraction*>::iterator, bool> ret;
98 >    int atid1, atid2;
99 >
100 >    // We only need to worry about the types that are actually in the simulation:
101 >
102 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
103 >
104 >    lj_->setSimulatedAtomTypes(atypes);
105 >    gb_->setSimulatedAtomTypes(atypes);
106 >    sticky_->setSimulatedAtomTypes(atypes);
107 >    eam_->setSimulatedAtomTypes(atypes);
108 >    sc_->setSimulatedAtomTypes(atypes);
109 >    morse_->setSimulatedAtomTypes(atypes);
110 >    electrostatic_->setSimInfo(info_);
111 >    electrostatic_->setSimulatedAtomTypes(atypes);
112 >    maw_->setSimulatedAtomTypes(atypes);
113 >    repulsivePower_->setSimulatedAtomTypes(atypes);
114 >
115 >    set<AtomType*>::iterator at;
116 >
117 >    for (at = atypes.begin(); at != atypes.end(); ++at) {
118      
119 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 <         atype1 = atomTypes->nextType(i1)) {
119 >      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120 >      //   atype1 = atomTypes->nextType(i1)) {
121        
122 <      // add it to the map:
123 <      AtomTypeProperties atp = atype1->getATP();    
124 <      
122 >      atype1 = *at;
123 >      atid1 = atype1->getIdent();
124 >      iHash_[atid1].resize(nTypes);
125 >      interactions_[atid1].resize(nTypes);
126 >
127 >      // add it to the map:      
128        pair<map<int,AtomType*>::iterator,bool> ret;    
129 <      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
129 >      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
130        if (ret.second == false) {
131          sprintf( painCave.errMsg,
132                   "InteractionManager already had a previous entry with ident %d\n",
133 <                 atp.ident);
133 >                 atype1->getIdent());
134          painCave.severity = OPENMD_INFO;
135          painCave.isFatal = 0;
136          simError();                
# Line 140 | Line 142 | namespace OpenMD {
142      map<int, AtomType*>::iterator it1, it2;
143      for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
144        atype1 = (*it1).second;
145 +      atid1 = atype1->getIdent();
146  
147        for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
148          atype2 = (*it2).second;
149 +        atid2 = atype2->getIdent();
150 +                              
151 +        iHash_[atid1][atid2] = 0;
152          
147 –        bool vdwExplicit = false;
148 –        bool metExplicit = false;
149 –        bool hbExplicit = false;
150 –                      
151 –        key = make_pair(atype1, atype2);
152 –        
153          if (atype1->isLennardJones() && atype2->isLennardJones()) {
154 <          interactions_[key].insert(lj_);
154 >          interactions_[atid1][atid2].insert(lj_);
155 >          iHash_[atid1][atid2] |= LJ_PAIR;
156          }
157          if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158 <          interactions_[key].insert(electrostatic_);
158 >          interactions_[atid1][atid2].insert(electrostatic_);
159 >          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
160          }
161          if (atype1->isSticky() && atype2->isSticky() ) {
162 <          interactions_[key].insert(sticky_);
162 >          interactions_[atid1][atid2].insert(sticky_);
163 >          iHash_[atid1][atid2] |= STICKY_PAIR;
164          }
165          if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166 <          interactions_[key].insert(sticky_);
166 >          interactions_[atid1][atid2].insert(sticky_);
167 >          iHash_[atid1][atid2] |= STICKY_PAIR;
168          }
169          if (atype1->isEAM() && atype2->isEAM() ) {
170 <          interactions_[key].insert(eam_);
170 >          interactions_[atid1][atid2].insert(eam_);
171 >          iHash_[atid1][atid2] |= EAM_PAIR;
172          }
173          if (atype1->isSC() && atype2->isSC() ) {
174 <          interactions_[key].insert(sc_);
174 >          interactions_[atid1][atid2].insert(sc_);
175 >          iHash_[atid1][atid2] |= SC_PAIR;
176          }
177          if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178 <          interactions_[key].insert(gb_);
178 >          interactions_[atid1][atid2].insert(gb_);
179 >          iHash_[atid1][atid2] |= GB_PAIR;
180          }
181          if ((atype1->isGayBerne() && atype2->isLennardJones())
182              || (atype1->isLennardJones() && atype2->isGayBerne())) {
183 <          interactions_[key].insert(gb_);
183 >          interactions_[atid1][atid2].insert(gb_);
184 >          iHash_[atid1][atid2] |= GB_PAIR;
185          }
186          
187          // look for an explicitly-set non-bonded interaction type using the
# Line 182 | Line 190 | namespace OpenMD {
190          
191          if (nbiType != NULL) {
192  
193 +          bool vdwExplicit = false;
194 +          bool metExplicit = false;
195 +          // bool hbExplicit = false;
196 +
197            if (nbiType->isLennardJones()) {
198              // We found an explicit Lennard-Jones interaction.  
199              // override all other vdw entries for this pair of atom types:
200              set<NonBondedInteraction*>::iterator it;
201 <            for (it = interactions_[key].begin();
202 <                 it != interactions_[key].end(); ++it) {
201 >            for (it = interactions_[atid1][atid2].begin();
202 >                 it != interactions_[atid1][atid2].end(); ++it) {
203                InteractionFamily ifam = (*it)->getFamily();
204 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204 >              if (ifam == VANDERWAALS_FAMILY) {
205 >                interactions_[atid1][atid2].erase(*it);
206 >                iHash_[atid1][atid2] ^= (*it)->getHash();
207 >              }
208              }
209 <            interactions_[key].insert(lj_);
209 >            interactions_[atid1][atid2].insert(lj_);
210 >            iHash_[atid1][atid2] |= LJ_PAIR;
211              vdwExplicit = true;
212            }
213            
# Line 209 | Line 225 | namespace OpenMD {
225              // We found an explicit Morse interaction.  
226              // override all other vdw entries for this pair of atom types:
227              set<NonBondedInteraction*>::iterator it;
228 <            for (it = interactions_[key].begin();
229 <                 it != interactions_[key].end(); ++it) {
228 >            for (it = interactions_[atid1][atid2].begin();
229 >                 it != interactions_[atid1][atid2].end(); ++it) {
230                InteractionFamily ifam = (*it)->getFamily();
231 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
231 >              if (ifam == VANDERWAALS_FAMILY) {
232 >                interactions_[atid1][atid2].erase(*it);
233 >                iHash_[atid1][atid2] ^= (*it)->getHash();
234 >              }
235              }
236 <            interactions_[key].insert(morse_);
236 >            interactions_[atid1][atid2].insert(morse_);
237 >            iHash_[atid1][atid2] |= MORSE_PAIR;
238 >            vdwExplicit = true;
239 >          }
240 >
241 >          if (nbiType->isRepulsivePower()) {
242 >            if (vdwExplicit) {
243 >              sprintf( painCave.errMsg,
244 >                       "InteractionManager::initialize found more than one "
245 >                       "explicit \n"
246 >                       "\tvan der Waals interaction for atom types %s - %s\n",
247 >                       atype1->getName().c_str(), atype2->getName().c_str());
248 >              painCave.severity = OPENMD_ERROR;
249 >              painCave.isFatal = 1;
250 >              simError();
251 >            }
252 >            // We found an explicit RepulsivePower interaction.  
253 >            // override all other vdw entries for this pair of atom types:
254 >            set<NonBondedInteraction*>::iterator it;
255 >            for (it = interactions_[atid1][atid2].begin();
256 >                 it != interactions_[atid1][atid2].end(); ++it) {
257 >              InteractionFamily ifam = (*it)->getFamily();
258 >              if (ifam == VANDERWAALS_FAMILY) {
259 >                interactions_[atid1][atid2].erase(*it);
260 >                iHash_[atid1][atid2] ^= (*it)->getHash();
261 >              }
262 >            }
263 >            interactions_[atid1][atid2].insert(repulsivePower_);
264 >            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
265              vdwExplicit = true;
266            }
267            
268 +          
269            if (nbiType->isEAM()) {
270              // We found an explicit EAM interaction.  
271              // override all other metallic entries for this pair of atom types:
272              set<NonBondedInteraction*>::iterator it;
273 <            for (it = interactions_[key].begin();
274 <                 it != interactions_[key].end(); ++it) {
273 >            for (it = interactions_[atid1][atid2].begin();
274 >                 it != interactions_[atid1][atid2].end(); ++it) {
275                InteractionFamily ifam = (*it)->getFamily();
276 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
276 >              if (ifam == METALLIC_FAMILY) {
277 >                interactions_[atid1][atid2].erase(*it);
278 >                iHash_[atid1][atid2] ^= (*it)->getHash();
279 >              }
280              }
281 <            interactions_[key].insert(eam_);
281 >            interactions_[atid1][atid2].insert(eam_);
282 >            iHash_[atid1][atid2] |= EAM_PAIR;
283              metExplicit = true;
284            }
285            
# Line 245 | Line 297 | namespace OpenMD {
297              // We found an explicit Sutton-Chen interaction.  
298              // override all other metallic entries for this pair of atom types:
299              set<NonBondedInteraction*>::iterator it;
300 <            for (it = interactions_[key].begin();
301 <                 it != interactions_[key].end(); ++it) {
300 >            for (it = interactions_[atid1][atid2].begin();
301 >                 it != interactions_[atid1][atid2].end(); ++it) {
302                InteractionFamily ifam = (*it)->getFamily();
303 <              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
303 >              if (ifam == METALLIC_FAMILY) {
304 >                interactions_[atid1][atid2].erase(*it);
305 >                iHash_[atid1][atid2] ^= (*it)->getHash();
306 >              }
307              }
308 <            interactions_[key].insert(sc_);
308 >            interactions_[atid1][atid2].insert(sc_);
309 >            iHash_[atid1][atid2] |= SC_PAIR;
310              metExplicit = true;
311            }
312            
# Line 268 | Line 324 | namespace OpenMD {
324              // We found an explicit MAW interaction.  
325              // override all other vdw entries for this pair of atom types:
326              set<NonBondedInteraction*>::iterator it;
327 <            for (it = interactions_[key].begin();
328 <                 it != interactions_[key].end(); ++it) {
327 >            for (it = interactions_[atid1][atid2].begin();
328 >                 it != interactions_[atid1][atid2].end(); ++it) {
329                InteractionFamily ifam = (*it)->getFamily();
330 <              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
330 >              if (ifam == VANDERWAALS_FAMILY) {
331 >                interactions_[atid1][atid2].erase(*it);
332 >                iHash_[atid1][atid2] ^= (*it)->getHash();
333 >              }
334              }
335 <            interactions_[key].insert(maw_);
335 >            interactions_[atid1][atid2].insert(maw_);
336 >            iHash_[atid1][atid2] |= MAW_PAIR;
337              vdwExplicit = true;
338            }        
339          }
# Line 281 | Line 341 | namespace OpenMD {
341      }
342      
343      
344 <    // make sure every pair of atom types in this simulation has a
345 <    // non-bonded interaction:
344 >    // Make sure every pair of atom types in this simulation has a
345 >    // non-bonded interaction.  If not, just inform the user.
346  
347      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
348      set<AtomType*>::iterator it, jt;
349 +
350      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
351        atype1 = (*it);
352 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
352 >      atid1 = atype1->getIdent();
353 >      for (jt = it; jt != simTypes.end(); ++jt) {
354          atype2 = (*jt);
355 <        key = make_pair(atype1, atype2);
355 >        atid1 = atype1->getIdent();
356          
357 <        if (interactions_[key].size() == 0) {
357 >        if (interactions_[atid1][atid2].size() == 0) {
358            sprintf( painCave.errMsg,
359 <                   "InteractionManager unable to find an appropriate non-bonded\n"
360 <                   "\tinteraction for atom types %s - %s\n",
359 >                   "InteractionManager could not find a matching non-bonded\n"
360 >                   "\tinteraction for atom types %s - %s\n"
361 >                   "\tProceeding without this interaction.\n",
362                     atype1->getName().c_str(), atype2->getName().c_str());
363            painCave.severity = OPENMD_INFO;
364 <          painCave.isFatal = 1;
364 >          painCave.isFatal = 0;
365            simError();
366          }
367        }
368      }
369  
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 –
370      initialized_ = true;
371    }
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 –    }
372  
373 <    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 <    }          
373 >  void InteractionManager::setCutoffRadius(RealType rcut) {
374      
375 <    if (simParams_->haveSwitchingFunctionType()) {
376 <      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_);
375 >    electrostatic_->setCutoffRadius(rcut);
376 >    eam_->setCutoffRadius(rcut);
377    }
378  
379 <  /**
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){
379 >  void InteractionManager::doPrePair(InteractionData &idat){
380      
381      if (!initialized_) initialize();
382 <          
383 <    DensityData ddat;
382 >        
383 >    // excluded interaction, so just return
384 >    if (idat.excluded) return;
385  
386 <    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;
386 >    int& iHash = iHash_[idat.atid1][idat.atid2];
387  
388 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
389 <    set<NonBondedInteraction*>::iterator it;
388 >    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389 >    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);
390  
391 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
392 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
393 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
394 <      }
395 <    }
391 >    // set<NonBondedInteraction*>::iterator it;
392 >
393 >    // for (it = interactions_[ idat.atypes ].begin();
394 >    //      it != interactions_[ idat.atypes ].end(); ++it){
395 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
396 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
397 >    //   }
398 >    // }
399      
400      return;    
401    }
402    
403 <  void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
403 >  void InteractionManager::doPreForce(SelfData &sdat){
404  
405      if (!initialized_) initialize();
406 <          
407 <    FunctionalData fdat;
406 >    
407 >    int& iHash = iHash_[sdat.atid][sdat.atid];
408  
409 <    fdat.atype = typeMap_[*atid];
410 <    fdat.rho = *rho;
521 <    fdat.frho = *frho;
522 <    fdat.dfrhodrho = *dfrhodrho;
409 >    if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
410 >    if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);
411  
412 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
525 <    set<NonBondedInteraction*>::iterator it;
412 >    // set<NonBondedInteraction*>::iterator it;
413      
414 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
415 <      if ((*it)->getFamily() == METALLIC_FAMILY) {
416 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
417 <      }
418 <    }
414 >    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
415 >    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
416 >    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
417 >    //   }
418 >    // }
419      
420      return;    
421    }
422  
423 <  void InteractionManager::doPair(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){
423 >  void InteractionManager::doPair(InteractionData &idat){
424      
425      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;
426  
427 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
569 <    set<NonBondedInteraction*>::iterator it;
427 >    int& iHash = iHash_[idat.atid1][idat.atid2];
428  
429 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
430 <      (*it)->calcForce(idat);
431 <    
432 <    for (int i = 0; i < 4; i++) {
575 <      vpair[i] = idat.vpair[i];
576 <      pot[i] = idat.pot[i];
577 <    }
429 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430 >      
431 >    // electrostatics still has to worry about indirect
432 >    // contributions from excluded pairs of atoms, but nothing else does:
433  
434 <    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 <    }
434 >    if (idat.excluded) return;
435  
436 <    return;    
437 <  }
436 >    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
437 >    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
438 >    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
439 >    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
440 >    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
441 >    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
442 >    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
443 >    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);
444  
445 <  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){
445 >    // set<NonBondedInteraction*>::iterator it;
446  
447 <    if (!initialized_) initialize();
448 <    
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);
447 >    // for (it = interactions_[ idat.atypes ].begin();
448 >    //      it != interactions_[ idat.atypes ].end(); ++it) {
449  
450 <    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
451 <    set<NonBondedInteraction*>::iterator it;
450 >    //   // electrostatics still has to worry about indirect
451 >    //   // contributions from excluded pairs of atoms:
452  
453 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
454 <      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
455 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
456 <      }
619 <    }
453 >    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
454 >    //     (*it)->calcForce(idat);
455 >    //   }
456 >    // }
457      
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 –
458      return;    
459    }
460  
461 <  void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
461 >  void InteractionManager::doSelfCorrection(SelfData &sdat){
462  
463      if (!initialized_) initialize();
464      
465 <    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);
465 >    int& iHash = iHash_[sdat.atid][sdat.atid];
466  
467 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
650 <    set<NonBondedInteraction*>::iterator it;
467 >    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468  
469 <    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();
469 >    // set<NonBondedInteraction*>::iterator it;
470  
471 +    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
472 +    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473 +    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
474 +    //   }
475 +    // }
476 +      
477      return;    
478    }
479  
480 +  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
481 +    if (!initialized_) initialize();
482 +    electrostatic_->ReciprocalSpaceSum(pot);
483 +  }
484  
485    RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
486      if (!initialized_) initialize();
487 <    
487 >
488      AtomType* atype = typeMap_[*atid];
489  
671 –    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
490      set<NonBondedInteraction*>::iterator it;
491      RealType cutoff = 0.0;
492      
493 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
494 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
493 >    for (it = interactions_[*atid][*atid].begin();
494 >         it != interactions_[*atid][*atid].end();
495 >         ++it)
496 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
497      return cutoff;    
498    }
499  
500    RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
501      if (!initialized_) initialize();
502      
503 <    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
503 >    int atid = atype->getIdent();
504 >
505      set<NonBondedInteraction*>::iterator it;
506      RealType cutoff = 0.0;
507      
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
509 <      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype));  
508 >    for (it = interactions_[atid][atid].begin();
509 >         it != interactions_[atid][atid].end(); ++it)
510 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));  
511      return cutoff;    
512    }
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 –
513   } //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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