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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

# Line 40 | Line 40
40   */
41  
42   #include "nonbonded/InteractionManager.hpp"
43 + #include "UseTheForce/doForces_interface.h"
44  
45   namespace OpenMD {
46 <
46 >
47 >  InteractionManager* InteractionManager::_instance = NULL;
48 >  SimInfo* InteractionManager::info_ = NULL;
49    bool InteractionManager::initialized_ = false;
50 <  RealType InteractionManager::rCut_ = -1.0;
51 <  RealType InteractionManager::rSwitch_ = -1.0;
52 <  ForceField* InteractionManager::forceField_ = NULL;  
53 <  InteractionManager* InteractionManager::_instance = NULL;
50 >
51 >  RealType InteractionManager::rCut_ = 0.0;
52 >  RealType InteractionManager::rSwitch_ = 0.0;
53 >  RealType InteractionManager::skinThickness_ = 0.0;
54 >  RealType InteractionManager::listRadius_ = 0.0;
55 >  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
56 >  SwitchingFunctionType InteractionManager::sft_ = cubic;
57 >  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
58 >  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
59 >
60    map<int, AtomType*> InteractionManager::typeMap_;
61    map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
62  
# Line 70 | Line 79 | namespace OpenMD {
79  
80    void InteractionManager::initialize() {
81      
82 +    ForceField* forceField_ = info_->getForceField();
83 +    
84      lj_->setForceField(forceField_);
85      gb_->setForceField(forceField_);
86      sticky_->setForceField(forceField_);
# Line 80 | Line 91 | namespace OpenMD {
91      maw_->setForceField(forceField_);
92  
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 = the atom itself
98 >    // 0 = topologically unconnected
99      // 1 = bonded together
100      // 2 = connected via a bend
101      // 3 = connected via a torsion
102  
103 <    vdwScale_[0] = 0.0;
103 >    vdwScale_[0] = 1.0;
104      vdwScale_[1] = fopts.getvdw12scale();
105      vdwScale_[2] = fopts.getvdw13scale();
106      vdwScale_[3] = fopts.getvdw14scale();
107  
108 <    electrostaticScale_[0] = 0.0;
108 >    electrostaticScale_[0] = 1.0;
109      electrostaticScale_[1] = fopts.getelectrostatic12scale();
110      electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 <    electrostaticScale_[3] = fopts.getelectrostatic14scale();
111 >    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112  
113      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
114      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
# Line 167 | Line 179 | namespace OpenMD {
179          // look for an explicitly-set non-bonded interaction type using the
180          // two atom types.
181          NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
182 +        
183 +        if (nbiType != NULL) {
184  
185 <        if (nbiType->isLennardJones()) {
186 <          // We found an explicit Lennard-Jones interaction.  
187 <          // override all other vdw entries for this pair of atom types:
188 <          set<NonBondedInteraction*>::iterator it;
189 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
190 <            InteractionFamily ifam = (*it)->getFamily();
191 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
185 >          if (nbiType->isLennardJones()) {
186 >            // We found an explicit Lennard-Jones interaction.  
187 >            // override all other vdw entries for this pair of atom types:
188 >            set<NonBondedInteraction*>::iterator it;
189 >            for (it = interactions_[key].begin();
190 >                 it != interactions_[key].end(); ++it) {
191 >              InteractionFamily ifam = (*it)->getFamily();
192 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
193 >            }
194 >            interactions_[key].insert(lj_);
195 >            vdwExplicit = true;
196            }
197 <          interactions_[key].insert(lj_);
198 <          vdwExplicit = true;
199 <        }
200 <
201 <        if (nbiType->isMorse()) {
202 <          if (vdwExplicit) {
203 <            sprintf( painCave.errMsg,
204 <                     "InteractionManager::initialize found more than one explicit\n"
205 <                     "\tvan der Waals interaction for atom types %s - %s\n",
206 <                     atype1->getName().c_str(), atype2->getName().c_str());
207 <            painCave.severity = OPENMD_ERROR;
208 <            painCave.isFatal = 1;
209 <            simError();
197 >          
198 >          if (nbiType->isMorse()) {
199 >            if (vdwExplicit) {
200 >              sprintf( painCave.errMsg,
201 >                       "InteractionManager::initialize found more than one "
202 >                       "explicit \n"
203 >                       "\tvan der Waals interaction for atom types %s - %s\n",
204 >                       atype1->getName().c_str(), atype2->getName().c_str());
205 >              painCave.severity = OPENMD_ERROR;
206 >              painCave.isFatal = 1;
207 >              simError();
208 >            }
209 >            // We found an explicit Morse interaction.  
210 >            // override all other vdw entries for this pair of atom types:
211 >            set<NonBondedInteraction*>::iterator it;
212 >            for (it = interactions_[key].begin();
213 >                 it != interactions_[key].end(); ++it) {
214 >              InteractionFamily ifam = (*it)->getFamily();
215 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
216 >            }
217 >            interactions_[key].insert(morse_);
218 >            vdwExplicit = true;
219            }
220 <          // We found an explicit Morse interaction.  
221 <          // override all other vdw entries for this pair of atom types:
222 <          set<NonBondedInteraction*>::iterator it;
223 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
224 <            InteractionFamily ifam = (*it)->getFamily();
225 <            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
220 >          
221 >          if (nbiType->isEAM()) {
222 >            // We found an explicit EAM interaction.  
223 >            // override all other metallic entries for this pair of atom types:
224 >            set<NonBondedInteraction*>::iterator it;
225 >            for (it = interactions_[key].begin();
226 >                 it != interactions_[key].end(); ++it) {
227 >              InteractionFamily ifam = (*it)->getFamily();
228 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
229 >            }
230 >            interactions_[key].insert(eam_);
231 >            metExplicit = true;
232            }
233 <          interactions_[key].insert(morse_);
234 <          vdwExplicit = true;
235 <        }
236 <
237 <        if (nbiType->isEAM()) {
238 <          // We found an explicit EAM interaction.  
239 <          // override all other metallic entries for this pair of atom types:
240 <          set<NonBondedInteraction*>::iterator it;
241 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
242 <            InteractionFamily ifam = (*it)->getFamily();
243 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
244 <          }
245 <          interactions_[key].insert(eam_);
246 <          metExplicit = true;
247 <        }
248 <
249 <        if (nbiType->isSC()) {
250 <          if (metExplicit) {
251 <            sprintf( painCave.errMsg,
252 <                     "InteractionManager::initialize found more than one explicit\n"
253 <                     "\tmetallic interaction for atom types %s - %s\n",
254 <                     atype1->getName().c_str(), atype2->getName().c_str());
222 <            painCave.severity = OPENMD_ERROR;
223 <            painCave.isFatal = 1;
224 <            simError();
233 >          
234 >          if (nbiType->isSC()) {
235 >            if (metExplicit) {
236 >              sprintf( painCave.errMsg,
237 >                       "InteractionManager::initialize found more than one "
238 >                       "explicit\n"
239 >                       "\tmetallic interaction for atom types %s - %s\n",
240 >                       atype1->getName().c_str(), atype2->getName().c_str());
241 >              painCave.severity = OPENMD_ERROR;
242 >              painCave.isFatal = 1;
243 >              simError();
244 >            }
245 >            // We found an explicit Sutton-Chen interaction.  
246 >            // override all other metallic entries for this pair of atom types:
247 >            set<NonBondedInteraction*>::iterator it;
248 >            for (it = interactions_[key].begin();
249 >                 it != interactions_[key].end(); ++it) {
250 >              InteractionFamily ifam = (*it)->getFamily();
251 >              if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
252 >            }
253 >            interactions_[key].insert(sc_);
254 >            metExplicit = true;
255            }
256 <          // We found an explicit Sutton-Chen interaction.  
257 <          // override all other metallic entries for this pair of atom types:
258 <          set<NonBondedInteraction*>::iterator it;
259 <          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
260 <            InteractionFamily ifam = (*it)->getFamily();
261 <            if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
262 <          }
263 <          interactions_[key].insert(sc_);
264 <          metExplicit = true;
256 >          
257 >          if (nbiType->isMAW()) {
258 >            if (vdwExplicit) {
259 >              sprintf( painCave.errMsg,
260 >                       "InteractionManager::initialize found more than one "
261 >                       "explicit\n"
262 >                       "\tvan der Waals interaction for atom types %s - %s\n",
263 >                       atype1->getName().c_str(), atype2->getName().c_str());
264 >              painCave.severity = OPENMD_ERROR;
265 >              painCave.isFatal = 1;
266 >              simError();
267 >            }
268 >            // We found an explicit MAW interaction.  
269 >            // override all other vdw entries for this pair of atom types:
270 >            set<NonBondedInteraction*>::iterator it;
271 >            for (it = interactions_[key].begin();
272 >                 it != interactions_[key].end(); ++it) {
273 >              InteractionFamily ifam = (*it)->getFamily();
274 >              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
275 >            }
276 >            interactions_[key].insert(maw_);
277 >            vdwExplicit = true;
278 >          }        
279          }
236 –
237 –        if (nbiType->isMAW()) {
238 –          if (vdwExplicit) {
239 –            sprintf( painCave.errMsg,
240 –                     "InteractionManager::initialize found more than one explicit\n"
241 –                     "\tvan der Waals interaction for atom types %s - %s\n",
242 –                     atype1->getName().c_str(), atype2->getName().c_str());
243 –            painCave.severity = OPENMD_ERROR;
244 –            painCave.isFatal = 1;
245 –            simError();
246 –          }
247 –          // We found an explicit MAW interaction.  
248 –          // override all other vdw entries for this pair of atom types:
249 –          set<NonBondedInteraction*>::iterator it;
250 –          for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) {
251 –            InteractionFamily ifam = (*it)->getFamily();
252 –            if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
253 –          }
254 –          interactions_[key].insert(maw_);
255 –          vdwExplicit = true;
256 –        }        
280        }
281      }
282      
283 <    // make sure every pair of atom types has a non-bonded interaction:
284 <    for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
285 <         atype1 = atomTypes->nextType(i1)) {
286 <      for (atype2 = atomTypes->beginType(i2); atype2 != NULL;
287 <           atype2 = atomTypes->nextType(i2)) {
283 >    
284 >    // make sure every pair of atom types in this simulation has a
285 >    // non-bonded interaction:
286 >
287 >    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
288 >    set<AtomType*>::iterator it, jt;
289 >    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
290 >      atype1 = (*it);
291 >      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
292 >        atype2 = (*jt);
293          key = make_pair(atype1, atype2);
294          
295          if (interactions_[key].size() == 0) {
# Line 275 | Line 303 | namespace OpenMD {
303          }
304        }
305      }
306 <  }
306 >
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 >
316 >    initialized_ = true;
317 >  }
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 +    }
370 +
371 +    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 +    }          
435 +    
436 +    if (simParams_->haveSwitchingFunctionType()) {
437 +      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_);
460 +  }
461 +
462 +  /**
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){
490      
491      if (!initialized_) initialize();
# Line 324 | Line 533 | namespace OpenMD {
533      return;    
534    }
535  
536 <  void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, int *topoDist, 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){
536 >  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){
537      
538      if (!initialized_) initialize();
539      
# Line 335 | Line 544 | namespace OpenMD {
544      idat.d = Vector3d(d);
545      idat.rij = *r;
546      idat.r2 = *r2;
338 –    idat.rcut = *rcut;
547      idat.sw = *sw;
548      idat.vdwMult = vdwScale_[*topoDist];
549      idat.electroMult = electrostaticScale_[*topoDist];
550 <    idat.pot = *pot;
551 <    idat.vpair = *vpair;
552 <    idat.f1 = Vector3d(f1);
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);
# Line 361 | Line 571 | namespace OpenMD {
571      for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
572        (*it)->calcForce(idat);
573      
574 <    f1[0] = idat.f1.x();
575 <    f1[1] = idat.f1.y();
576 <    f1[2] = idat.f1.z();
577 <    
368 <    t1[0] = idat.t1.x();
369 <    t1[1] = idat.t1.y();
370 <    t1[2] = idat.t1.z();
371 <    
372 <    t2[0] = idat.t2.x();
373 <    t2[1] = idat.t2.y();
374 <    t2[2] = idat.t2.z();
574 >    for (int i = 0; i < 4; i++) {
575 >      vpair[i] = idat.vpair[i];
576 >      pot[i] = idat.pot[i];
577 >    }
578  
579 +    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 +    }
584 +
585      return;    
586    }
587  
# Line 390 | Line 599 | namespace OpenMD {
599      skdat.skippedCharge2 = *skippedCharge2;
600      skdat.sw = *sw;
601      skdat.electroMult = *electroMult;
602 <    skdat.pot = *pot;
603 <    skdat.vpair = *vpair;
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);
# Line 407 | Line 618 | namespace OpenMD {
618        }
619      }
620      
621 <    f1[0] = skdat.f1.x();
622 <    f1[1] = skdat.f1.y();
623 <    f1[2] = skdat.f1.z();
624 <    
414 <    t1[0] = skdat.t1.x();
415 <    t1[1] = skdat.t1.y();
416 <    t1[2] = skdat.t1.z();
417 <    
418 <    t2[0] = skdat.t2.x();
419 <    t2[1] = skdat.t2.y();
420 <    t2[2] = skdat.t2.z();
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 +
632      return;    
633    }
634  
# Line 431 | Line 641 | namespace OpenMD {
641      scdat.atype = typeMap_[*atid];
642      scdat.eFrame = Mat3x3d(eFrame);
643      scdat.skippedCharge = *skippedCharge;
644 <    scdat.pot = *pot;
644 >    for (int i = 0; i < 4; i++){
645 >      scdat.pot[i] = pot[i];
646 >    }    
647      scdat.t = Vector3d(t);
648  
649      pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype);
# Line 442 | Line 654 | namespace OpenMD {
654          dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat);
655        }
656      }
657 <        
657 >      
658      t[0] = scdat.t.x();
659      t[1] = scdat.t.y();
660      t[2] = scdat.t.z();
# Line 477 | Line 689 | namespace OpenMD {
689      return cutoff;    
690    }
691  
480 –
481 –  void InteractionManager::setSwitch(RealType *rIn, RealType *rOut) {
482 –    switcher_->setSwitch(*rIn, *rOut);    
483 –  }
484 –
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);    
694 >    bool isr = switcher_->getSwitch( *r2 , *sw, *dswdr, *r);    
695      *in_switching_region = (int)isr;
696    }
697  
# Line 498 | Line 705 | extern "C" {
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)
501 – #define fortranSetSwitch FC_FUNC(set_switch, SET_SWITCH)
708   #define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH)
709  
710    void fortranDoPrePair(int *atid1, int *atid2, RealType *rij,
# Line 515 | Line 721 | extern "C" {
721                                                                dfrhodrho);    
722    }
723    
724 <  void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r,
725 <                     RealType *r2, RealType *rcut, RealType *sw, int *topoDist,
726 <                     RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1,
727 <                     RealType *eFrame2, RealType *A1, RealType *A2,
728 <                     RealType *t1, RealType *t2, RealType *rho1, RealType *rho2,
729 <                     RealType *dfrho1, RealType *dfrho2, RealType *fshift1,
730 <                     RealType *fshift2){
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,
733 <                                                          r2, rcut, sw, topoDist,
528 <                                                          pot, vpair, f1,
732 >    return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r, r2,
733 >                                                          sw, topoDist, A1, A2,
734                                                            eFrame1, eFrame2,
735 <                                                          A1, A2, t1, t2, rho1,
736 <                                                          rho2, dfrho1, dfrho2,
735 >                                                          vpair, pot,
736 >                                                          f1, t1, t2,
737 >                                                          rho1, rho2,
738 >                                                          dfrho1, dfrho2,
739                                                            fshift1, fshift2);
740    }
741    
# Line 563 | Line 770 | extern "C" {
770    }
771  
772    void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r,
773 <                        int *in_switching_region) {
567 <    
773 >                        int *in_switching_region) {    
774      return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r,
775                                                               in_switching_region);
776 <  }
571 <
572 <  void fortranSetSwitch(RealType *rIn, RealType *rOut) {    
573 <    return OpenMD::InteractionManager::Instance()->setSwitch(rIn, rOut);
574 <  }
575 <  
776 >  }  
777   }

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