ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/nonbonded/InteractionManager.cpp
(Generate patch)

Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1504 by gezelter, Sat Oct 2 20:41:53 2010 UTC vs.
Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

# Line 42 | Line 42 | namespace OpenMD {
42   #include "nonbonded/InteractionManager.hpp"
43  
44   namespace OpenMD {
45 <
45 >
46 >  InteractionManager* InteractionManager::_instance = NULL;
47 >  SimInfo* InteractionManager::info_ = NULL;
48    bool InteractionManager::initialized_ = false;
49 <  ForceField* InteractionManager::forceField_ = NULL;  
50 <  InteractionManager* InteractionManager::_instance = NULL;
49 >
50 >  RealType InteractionManager::rCut_ = 0.0;
51 >  RealType InteractionManager::rSwitch_ = 0.0;
52 >  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
53 >  SwitchingFunctionType InteractionManager::sft_ = cubic;
54 >  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
55 >  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
56 >
57    map<int, AtomType*> InteractionManager::typeMap_;
58    map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
59 +
60 +  LJ* InteractionManager::lj_ = new LJ();
61 +  GB* InteractionManager::gb_ = new GB();
62 +  Sticky* InteractionManager::sticky_ = new Sticky();
63 +  Morse* InteractionManager::morse_ = new Morse();
64 +  EAM* InteractionManager::eam_ = new EAM();
65 +  SC* InteractionManager::sc_ = new SC();
66 +  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) {
# Line 58 | Line 76 | namespace OpenMD {
76  
77    void InteractionManager::initialize() {
78      
79 <    lj_ = new LJ();
80 <    gb_ = new GB();
63 <    sticky_ = new Sticky();
64 <    eam_ = new EAM();
65 <    sc_ = new SC();
66 <    morse_ = new Morse();
67 <    electrostatic_ = new Electrostatic();
68 <
79 >    ForceField* forceField_ = info_->getForceField();
80 >    
81      lj_->setForceField(forceField_);
82      gb_->setForceField(forceField_);
83      sticky_->setForceField(forceField_);
# Line 73 | Line 85 | namespace OpenMD {
85      sc_->setForceField(forceField_);
86      morse_->setForceField(forceField_);
87      electrostatic_->setForceField(forceField_);
88 +    maw_->setForceField(forceField_);
89  
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 +
110      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
111      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
112      AtomType* atype1;
# Line 143 | Line 176 | namespace OpenMD {
176          // look for an explicitly-set non-bonded interaction type using the
177          // two atom types.
178          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
179 +        
180 +        if (nbiType != NULL) {
181  
182 <        if (nbiType->isLennardJones()) {
183 <          // We found an explicit Lennard-Jones interaction.  
184 <          // override all other vdw entries for this pair of atom types:
185 <          set<NonBondedInteraction*>::iterator it;
186 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
187 <            InteractionFamily ifam = (*it)->getFamily();
188 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
182 >          if (nbiType->isLennardJones()) {
183 >            // We found an explicit Lennard-Jones interaction.  
184 >            // override all other vdw entries for this pair of atom types:
185 >            set<NonBondedInteraction*>::iterator it;
186 >            for (it = interactions_[key].begin();
187 >                 it != interactions_[key].end(); ++it) {
188 >              InteractionFamily ifam = (*it)->getFamily();
189 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
190 >            }
191 >            interactions_[key].insert(lj_);
192 >            vdwExplicit = true;
193            }
194 <          interactions_[key].insert(lj_);
195 <          vdwExplicit = true;
196 <        }
197 <
198 <        if (nbiType->isMorse()) {
199 <          if (vdwExplicit) {
200 <            sprintf( painCave.errMsg,
201 <                     "InteractionManager::initialize found more than one explicit\n"
202 <                     "\tvan der Waals interaction for atom types %s - %s\n",
203 <                     atype1->getName().c_str(), atype2->getName().c_str());
204 <            painCave.severity = OPENMD_ERROR;
205 <            painCave.isFatal = 1;
206 <            simError();
194 >          
195 >          if (nbiType->isMorse()) {
196 >            if (vdwExplicit) {
197 >              sprintf( painCave.errMsg,
198 >                       "InteractionManager::initialize found more than one "
199 >                       "explicit \n"
200 >                       "\tvan der Waals interaction for atom types %s - %s\n",
201 >                       atype1->getName().c_str(), atype2->getName().c_str());
202 >              painCave.severity = OPENMD_ERROR;
203 >              painCave.isFatal = 1;
204 >              simError();
205 >            }
206 >            // We found an explicit Morse interaction.  
207 >            // override all other vdw entries for this pair of atom types:
208 >            set<NonBondedInteraction*>::iterator it;
209 >            for (it = interactions_[key].begin();
210 >                 it != interactions_[key].end(); ++it) {
211 >              InteractionFamily ifam = (*it)->getFamily();
212 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
213 >            }
214 >            interactions_[key].insert(morse_);
215 >            vdwExplicit = true;
216            }
217 <          // We found an explicit Morse interaction.  
218 <          // override all other vdw entries for this pair of atom types:
219 <          set<NonBondedInteraction*>::iterator it;
220 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
221 <            InteractionFamily ifam = (*it)->getFamily();
222 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
217 >          
218 >          if (nbiType->isEAM()) {
219 >            // We found an explicit EAM interaction.  
220 >            // override all other metallic entries for this pair of atom types:
221 >            set<NonBondedInteraction*>::iterator it;
222 >            for (it = interactions_[key].begin();
223 >                 it != interactions_[key].end(); ++it) {
224 >              InteractionFamily ifam = (*it)->getFamily();
225 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
226 >            }
227 >            interactions_[key].insert(eam_);
228 >            metExplicit = true;
229            }
230 <          interactions_[key].insert(morse_);
231 <          vdwExplicit = true;
232 <        }
233 <
234 <        if (nbiType->isEAM()) {
235 <          // We found an explicit EAM interaction.  
236 <          // override all other metallic entries for this pair of atom types:
237 <          set<NonBondedInteraction*>::iterator it;
238 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
239 <            InteractionFamily ifam = (*it)->getFamily();
240 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
241 <          }
242 <          interactions_[key].insert(eam_);
243 <          metExplicit = true;
244 <        }
245 <
246 <        if (nbiType->isSC()) {
247 <          if (metExplicit) {
248 <            sprintf( painCave.errMsg,
249 <                     "InteractionManager::initialize found more than one explicit\n"
250 <                     "\tmetallic interaction for atom types %s - %s\n",
251 <                     atype1->getName().c_str(), atype2->getName().c_str());
198 <            painCave.severity = OPENMD_ERROR;
199 <            painCave.isFatal = 1;
200 <            simError();
230 >          
231 >          if (nbiType->isSC()) {
232 >            if (metExplicit) {
233 >              sprintf( painCave.errMsg,
234 >                       "InteractionManager::initialize found more than one "
235 >                       "explicit\n"
236 >                       "\tmetallic interaction for atom types %s - %s\n",
237 >                       atype1->getName().c_str(), atype2->getName().c_str());
238 >              painCave.severity = OPENMD_ERROR;
239 >              painCave.isFatal = 1;
240 >              simError();
241 >            }
242 >            // We found an explicit Sutton-Chen interaction.  
243 >            // override all other metallic entries for this pair of atom types:
244 >            set<NonBondedInteraction*>::iterator it;
245 >            for (it = interactions_[key].begin();
246 >                 it != interactions_[key].end(); ++it) {
247 >              InteractionFamily ifam = (*it)->getFamily();
248 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
249 >            }
250 >            interactions_[key].insert(sc_);
251 >            metExplicit = true;
252            }
253 <          // We found an explicit Sutton-Chen interaction.  
254 <          // override all other metallic entries for this pair of atom types:
255 <          set<NonBondedInteraction*>::iterator it;
256 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
257 <            InteractionFamily ifam = (*it)->getFamily();
258 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
259 <          }
260 <          interactions_[key].insert(sc_);
261 <          metExplicit = true;
253 >          
254 >          if (nbiType->isMAW()) {
255 >            if (vdwExplicit) {
256 >              sprintf( painCave.errMsg,
257 >                       "InteractionManager::initialize found more than one "
258 >                       "explicit\n"
259 >                       "\tvan der Waals interaction for atom types %s - %s\n",
260 >                       atype1->getName().c_str(), atype2->getName().c_str());
261 >              painCave.severity = OPENMD_ERROR;
262 >              painCave.isFatal = 1;
263 >              simError();
264 >            }
265 >            // We found an explicit MAW interaction.  
266 >            // override all other vdw entries for this pair of atom types:
267 >            set<NonBondedInteraction*>::iterator it;
268 >            for (it = interactions_[key].begin();
269 >                 it != interactions_[key].end(); ++it) {
270 >              InteractionFamily ifam = (*it)->getFamily();
271 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
272 >            }
273 >            interactions_[key].insert(maw_);
274 >            vdwExplicit = true;
275 >          }        
276          }
277        }
278      }
279      
280 <    // make sure every pair of atom types has a non-bonded interaction:
281 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
282 <         atype1 = atomTypes->nextType(i1)) {
283 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
284 <           atype2 = atomTypes->nextType(i2)) {
280 >    
281 >    // make sure every pair of atom types in this simulation has a
282 >    // non-bonded interaction:
283 >
284 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
285 >    set<AtomType*>::iterator it, jt;
286 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
287 >      atype1 = (*it);
288 >      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
289 >        atype2 = (*jt);
290          key = make_pair(atype1, atype2);
291          
292          if (interactions_[key].size() == 0) {
# Line 230 | Line 300 | namespace OpenMD {
300          }
301        }
302      }
303 <  }
303 >
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 >
311 >    initialized_ = true;
312 >  }
313    
314 <  void InteractionManager::do_prepair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){
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 <    if (!initialized_) initialize();
334 <          
335 <    DensityData ddat;
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 >    }
365  
366 <    ddat.atype1 = typeMap_[*atid1];
367 <    ddat.atype2 = typeMap_[*atid2];
368 <    ddat.rij = *rij;
369 <    ddat.rho_i_at_j = *rho_i_at_j;
370 <    ddat.rho_j_at_i = *rho_j_at_i;
366 >    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 <    pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2);
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 >    }          
430 >    
431 >    if (simParams_->haveSwitchingFunctionType()) {
432 >      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_);
455 >  }
456 >
457 >  void InteractionManager::doPrePair(InteractionData idat){
458 >    
459 >    if (!initialized_) initialize();
460 >        
461      set<NonBondedInteraction*>::iterator it;
462  
463 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
463 >    for (it = interactions_[ idat.atypes ].begin();
464 >         it != interactions_[ idat.atypes ].end(); ++it){
465        if ((*it)->getFamily() == METALLIC_FAMILY) {
466 <        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat);
466 >        dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
467        }
468      }
469      
470      return;    
471    }
472    
473 <  void InteractionManager::do_preforce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){
473 >  void InteractionManager::doPreForce(SelfData sdat){
474  
475      if (!initialized_) initialize();
476 <          
477 <    FunctionalData fdat;
264 <
265 <    fdat.atype = typeMap_[*atid];
266 <    fdat.rho = *rho;
267 <    fdat.frho = *frho;
268 <    fdat.dfrhodrho = *dfrhodrho;
269 <
270 <    pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype);
476 >    
477 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
478      set<NonBondedInteraction*>::iterator it;
479      
480      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
481        if ((*it)->getFamily() == METALLIC_FAMILY) {
482 <        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat);
482 >        dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
483        }
484      }
485      
486      return;    
487    }
488  
489 <  void InteractionManager::do_pair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult,RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){
489 >  void InteractionManager::doPair(InteractionData idat){
490      
491      if (!initialized_) initialize();
492 <    
286 <    InteractionData idat;
287 <    
288 <    idat.atype1 = typeMap_[*atid1];
289 <    idat.atype2 = typeMap_[*atid2];
290 <    idat.d = Vector3d(d);
291 <    idat.rij = *r;
292 <    idat.r2 = *r2;
293 <    idat.rcut = *rcut;
294 <    idat.sw = *sw;
295 <    idat.vdwMult = *vdwMult;
296 <    idat.electroMult = *electroMult;
297 <    idat.pot = *pot;
298 <    idat.vpair = *vpair;
299 <    idat.f1 = Vector3d(f1);
300 <    idat.eFrame1 = Mat3x3d(eFrame1);
301 <    idat.eFrame2 = Mat3x3d(eFrame2);
302 <    idat.A1 = RotMat3x3d(A1);
303 <    idat.A2 = RotMat3x3d(A2);
304 <    idat.t1 = Vector3d(t1);
305 <    idat.t2 = Vector3d(t2);
306 <    idat.rho1 = *rho1;
307 <    idat.rho2 = *rho2;
308 <    idat.dfrho1 = *dfrho1;
309 <    idat.dfrho2 = *dfrho2;
310 <    idat.fshift1 = *fshift1;
311 <    idat.fshift2 = *fshift2;
312 <
313 <    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
492 >  
493      set<NonBondedInteraction*>::iterator it;
494  
495 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
495 >    for (it = interactions_[ idat.atypes ].begin();
496 >         it != interactions_[ idat.atypes ].end(); ++it)
497        (*it)->calcForce(idat);
498      
319 –    f1[0] = idat.f1.x();
320 –    f1[1] = idat.f1.y();
321 –    f1[2] = idat.f1.z();
322 –    
323 –    t1[0] = idat.t1.x();
324 –    t1[1] = idat.t1.y();
325 –    t1[2] = idat.t1.z();
326 –    
327 –    t2[0] = idat.t2.x();
328 –    t2[1] = idat.t2.y();
329 –    t2[2] = idat.t2.z();
330 –
499      return;    
500    }
501  
502 <  void InteractionManager::do_skip_correction(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){
502 >  void InteractionManager::doSkipCorrection(InteractionData idat){
503  
504 <    if (!initialized_) initialize();
504 >    if (!initialized_) initialize();  
505      
338 –    SkipCorrectionData skdat;
339 –    
340 –    skdat.atype1 = typeMap_[*atid1];
341 –    skdat.atype2 = typeMap_[*atid2];
342 –    skdat.d = Vector3d(d);
343 –    skdat.rij = *r;
344 –    skdat.skippedCharge1 = *skippedCharge1;
345 –    skdat.skippedCharge2 = *skippedCharge2;
346 –    skdat.sw = *sw;
347 –    skdat.electroMult = *electroMult;
348 –    skdat.pot = *pot;
349 –    skdat.vpair = *vpair;
350 –    skdat.f1 = Vector3d(f1);
351 –    skdat.eFrame1 = Mat3x3d(eFrame1);
352 –    skdat.eFrame2 = Mat3x3d(eFrame2);
353 –    skdat.t1 = Vector3d(t1);
354 –    skdat.t2 = Vector3d(t2);
355 –
356 –    pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2);
506      set<NonBondedInteraction*>::iterator it;
507  
508 <    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
508 >    for (it = interactions_[ idat.atypes ].begin();
509 >         it != interactions_[ idat.atypes ].end(); ++it){
510        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
511 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat);
511 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
512        }
513      }
514      
365 –    f1[0] = skdat.f1.x();
366 –    f1[1] = skdat.f1.y();
367 –    f1[2] = skdat.f1.z();
368 –    
369 –    t1[0] = skdat.t1.x();
370 –    t1[1] = skdat.t1.y();
371 –    t1[2] = skdat.t1.z();
372 –    
373 –    t2[0] = skdat.t2.x();
374 –    t2[1] = skdat.t2.y();
375 –    t2[2] = skdat.t2.z();
376 –
515      return;    
516    }
517  
518 <  void InteractionManager::do_self_correction(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){
518 >  void InteractionManager::doSelfCorrection(SelfData sdat){
519  
520      if (!initialized_) initialize();
521      
522 <    SelfCorrectionData scdat;
385 <    
386 <    scdat.atype = typeMap_[*atid];
387 <    scdat.eFrame = Mat3x3d(eFrame);
388 <    scdat.skippedCharge = *skippedCharge;
389 <    scdat.pot = *pot;
390 <    scdat.t = Vector3d(t);
391 <
392 <    pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
522 >    pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
523      set<NonBondedInteraction*>::iterator it;
524  
525      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
526        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
527 <        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
527 >        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
528        }
529      }
530 <        
401 <    t[0] = scdat.t.x();
402 <    t[1] = scdat.t.y();
403 <    t[2] = scdat.t.z();
404 <
530 >      
531      return;    
532    }
533  
534 < } //end namespace OpenMD
535 <
410 < extern "C" {
411 <  
412 < #define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR)
413 < #define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE)
414 < #define fortranDoPair FC_FUNC(do_pair, DO_PAIR)
415 < #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION)
416 < #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION)
417 < #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF)
418 <
419 <  void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
420 <                        RealType *rho_i_at_j, RealType *rho_j_at_i) {
421 <            
422 <    return OpenMD::InteractionManager::Instance()->do_prepair(atid1, atid2, rij,
423 <                                                              rho_i_at_j,  
424 <                                                              rho_j_at_i);
425 <  }
426 <  void fortranDoPreforce(int *atid, RealType *rho, RealType *frho,
427 <                         RealType *dfrhodrho) {  
534 >  RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
535 >    if (!initialized_) initialize();
536      
537 <    return OpenMD::InteractionManager::Instance()->do_preforce(atid, rho, frho,
430 <                                                               dfrhodrho);    
431 <  }
432 <  
433 <  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r,
434 <                     RealType *r2, RealType *rcut, RealType *sw,
435 <                     RealType *vdwMult, RealType *electroMult, RealType *pot,
436 <                     RealType *vpair, RealType *f1, RealType *eFrame1,
437 <                     RealType *eFrame2, RealType *A1, RealType *A2,
438 <                     RealType *t1, RealType *t2, RealType *rho1, RealType *rho2,
439 <                     RealType *dfrho1, RealType *dfrho2, RealType *fshift1,
440 <                     RealType *fshift2){
441 <    
442 <    return OpenMD::InteractionManager::Instance()->do_pair(atid1, atid2, d, r, r2, rcut,
443 <                                                           sw, vdwMult, electroMult, pot,
444 <                                                           vpair, f1, eFrame1, eFrame2,
445 <                                                           A1, A2, t1, t2, rho1, rho2,
446 <                                                           dfrho1, dfrho2, fshift1, fshift2);
447 <  }
537 >    AtomType* atype = typeMap_[*atid];
538  
539 <  void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r,
540 <                               RealType *skippedCharge1, RealType *skippedCharge2,
541 <                               RealType *sw, RealType *electroMult, RealType *pot,
452 <                               RealType *vpair, RealType *f1,
453 <                               RealType *eFrame1, RealType *eFrame2,
454 <                               RealType *t1, RealType *t2){
539 >    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
540 >    set<NonBondedInteraction*>::iterator it;
541 >    RealType cutoff = 0.0;
542      
543 <    return OpenMD::InteractionManager::Instance()->do_skip_correction(atid1, atid2, d, r,
544 <                                                                      skippedCharge1,
545 <                                                                      skippedCharge2,
459 <                                                                      sw, electroMult, pot,
460 <                                                                      vpair, f1, eFrame1,
461 <                                                                      eFrame2, t1, t2);
543 >    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
544 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
545 >    return cutoff;    
546    }
547  
548 <  void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge,
549 <                               RealType *pot, RealType *t) {
548 >  RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
549 >    if (!initialized_) initialize();
550      
551 <    return OpenMD::InteractionManager::Instance()->do_self_correction(atid, eFrame,
552 <                                                                      skippedCharge,
553 <                                                                      pot, t);
551 >    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
552 >    set<NonBondedInteraction*>::iterator it;
553 >    RealType cutoff = 0.0;
554 >    
555 >    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
556 >      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));  
557 >    return cutoff;    
558    }
559 <  RealType fortranGetCutoff() {
472 <    return OpenMD::InteractionManager::Instance()->getCutoff();
473 <  }
474 < }
559 > } //end namespace OpenMD

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines