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Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

# Line 36 | Line 36
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).                        
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   /**
# Line 75 | Line 76 | namespace OpenMD {
76    /**
77     * setupCutoffs
78     *
79 <   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81     *
82     * cutoffRadius : realType
83     *  If the cutoffRadius was explicitly set, use that value.
# Line 85 | Line 87 | namespace OpenMD {
87     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88     *      Use the maximum suggested value that was found.
89     *
90 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92     *      If cutoffMethod was explicitly set, use that choice.
93     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94     *
95     * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96     *      If cutoffPolicy was explicitly set, use that choice.
97     *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 +   *
99 +   * switchingRadius : realType
100 +   *  If the cutoffMethod was set to SWITCHED:
101 +   *      If the switchingRadius was explicitly set, use that value
102 +   *          (but do a sanity check first).
103 +   *      If the switchingRadius was not explicitly set: use 0.85 *
104 +   *      cutoffRadius_
105 +   *  If the cutoffMethod was not set to SWITCHED:
106 +   *      Set switchingRadius equal to cutoffRadius for safety.
107     */
108    void ForceManager::setupCutoffs() {
109      
110      Globals* simParams_ = info_->getSimParams();
111      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 +    int mdFileVersion;
113      
114 +    if (simParams_->haveMDfileVersion())
115 +      mdFileVersion = simParams_->getMDfileVersion();
116 +    else
117 +      mdFileVersion = 0;
118 +  
119      if (simParams_->haveCutoffRadius()) {
120        rCut_ = simParams_->getCutoffRadius();
121      } else {      
# Line 130 | Line 148 | namespace OpenMD {
148      }
149  
150      fDecomp_->setUserCutoff(rCut_);
151 +    interactionMan_->setCutoffRadius(rCut_);
152  
153      map<string, CutoffMethod> stringToCutoffMethod;
154      stringToCutoffMethod["HARD"] = HARD;
# Line 154 | Line 173 | namespace OpenMD {
173          cutoffMethod_ = i->second;
174        }
175      } else {
176 <      sprintf(painCave.errMsg,
177 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
178 <              "\tOpenMD will use SHIFTED_FORCE.\n");
179 <      painCave.isFatal = 0;
180 <      painCave.severity = OPENMD_INFO;
181 <      simError();
182 <      cutoffMethod_ = SHIFTED_FORCE;        
176 >      if (mdFileVersion > 1) {
177 >        sprintf(painCave.errMsg,
178 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179 >                "\tOpenMD will use SHIFTED_FORCE.\n");
180 >        painCave.isFatal = 0;
181 >        painCave.severity = OPENMD_INFO;
182 >        simError();
183 >        cutoffMethod_ = SHIFTED_FORCE;        
184 >      } else {
185 >        // handle the case where the old file version was in play
186 >        // (there should be no cutoffMethod, so we have to deduce it
187 >        // from other data).        
188 >
189 >        sprintf(painCave.errMsg,
190 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
192 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193 >                "\tbehavior of the older (version 1) code.  To remove this\n"
194 >                "\twarning, add an explicit cutoffMethod and change the top\n"
195 >                "\tof the file so that it begins with <OpenMD version=2>\n");
196 >        painCave.isFatal = 0;
197 >        painCave.severity = OPENMD_WARNING;
198 >        simError();            
199 >                
200 >        // The old file version tethered the shifting behavior to the
201 >        // electrostaticSummationMethod keyword.
202 >        
203 >        if (simParams_->haveElectrostaticSummationMethod()) {
204 >          string myMethod = simParams_->getElectrostaticSummationMethod();
205 >          toUpper(myMethod);
206 >        
207 >          if (myMethod == "SHIFTED_POTENTIAL") {
208 >            cutoffMethod_ = SHIFTED_POTENTIAL;
209 >          } else if (myMethod == "SHIFTED_FORCE") {
210 >            cutoffMethod_ = SHIFTED_FORCE;
211 >          }
212 >        
213 >          if (simParams_->haveSwitchingRadius())
214 >            rSwitch_ = simParams_->getSwitchingRadius();
215 >
216 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217 >            if (simParams_->haveSwitchingRadius()){
218 >              sprintf(painCave.errMsg,
219 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220 >                      "\tA value was set for the switchingRadius\n"
221 >                      "\teven though the electrostaticSummationMethod was\n"
222 >                      "\tset to %s\n", myMethod.c_str());
223 >              painCave.severity = OPENMD_WARNING;
224 >              painCave.isFatal = 1;
225 >              simError();            
226 >            }
227 >          }
228 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
229 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
230 >              sprintf(painCave.errMsg,
231 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232 >                      "\tcutoffRadius and switchingRadius are set to the\n"
233 >                      "\tsame value.  OpenMD will use shifted force\n"
234 >                      "\tpotentials instead of switching functions.\n");
235 >              painCave.isFatal = 0;
236 >              painCave.severity = OPENMD_WARNING;
237 >              simError();            
238 >            } else {
239 >              cutoffMethod_ = SHIFTED_POTENTIAL;
240 >              sprintf(painCave.errMsg,
241 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242 >                      "\tcutoffRadius and switchingRadius are set to the\n"
243 >                      "\tsame value.  OpenMD will use shifted potentials\n"
244 >                      "\tinstead of switching functions.\n");
245 >              painCave.isFatal = 0;
246 >              painCave.severity = OPENMD_WARNING;
247 >              simError();            
248 >            }
249 >          }
250 >        }
251 >      }
252      }
253  
254      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 168 | Line 256 | namespace OpenMD {
256      stringToCutoffPolicy["MAX"] = MAX;
257      stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
258  
259 <    std::string cutPolicy;
259 >    string cutPolicy;
260      if (forceFieldOptions_.haveCutoffPolicy()){
261        cutPolicy = forceFieldOptions_.getCutoffPolicy();
262      }else if (simParams_->haveCutoffPolicy()) {
# Line 201 | Line 289 | namespace OpenMD {
289        simError();
290        cutoffPolicy_ = TRADITIONAL;        
291      }
204 –    fDecomp_->setCutoffPolicy(cutoffPolicy_);
205 –  }
292  
293 <  /**
294 <   * setupSwitching
209 <   *
210 <   * Sets the values of switchingRadius and
211 <   *  If the switchingRadius was explicitly set, use that value (but check it)
212 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
213 <   */
214 <  void ForceManager::setupSwitching() {
215 <    Globals* simParams_ = info_->getSimParams();
216 <
293 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
294 >        
295      // create the switching function object:
296 +
297      switcher_ = new SwitchingFunction();
298 <    
299 <    if (simParams_->haveSwitchingRadius()) {
300 <      rSwitch_ = simParams_->getSwitchingRadius();
301 <      if (rSwitch_ > rCut_) {        
298 >  
299 >    if (cutoffMethod_ == SWITCHED) {
300 >      if (simParams_->haveSwitchingRadius()) {
301 >        rSwitch_ = simParams_->getSwitchingRadius();
302 >        if (rSwitch_ > rCut_) {        
303 >          sprintf(painCave.errMsg,
304 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306 >          painCave.isFatal = 1;
307 >          painCave.severity = OPENMD_ERROR;
308 >          simError();
309 >        }
310 >      } else {      
311 >        rSwitch_ = 0.85 * rCut_;
312          sprintf(painCave.errMsg,
313 <                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
314 <                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
315 <        painCave.isFatal = 1;
316 <        painCave.severity = OPENMD_ERROR;
313 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316 >        painCave.isFatal = 0;
317 >        painCave.severity = OPENMD_WARNING;
318          simError();
319        }
320 <    } else {      
321 <      rSwitch_ = 0.85 * rCut_;
322 <      sprintf(painCave.errMsg,
323 <              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
324 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
325 <              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
326 <      painCave.isFatal = 0;
327 <      painCave.severity = OPENMD_WARNING;
328 <      simError();
329 <    }          
320 >    } else {
321 >      if (mdFileVersion > 1) {
322 >        // throw an error if we define a switching radius and don't need one.
323 >        // older file versions should not do this.
324 >        if (simParams_->haveSwitchingRadius()) {
325 >          map<string, CutoffMethod>::const_iterator it;
326 >          string theMeth;
327 >          for (it = stringToCutoffMethod.begin();
328 >               it != stringToCutoffMethod.end(); ++it) {
329 >            if (it->second == cutoffMethod_) {
330 >              theMeth = it->first;
331 >              break;
332 >            }
333 >          }
334 >          sprintf(painCave.errMsg,
335 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
337 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
338 >          painCave.isFatal = 0;
339 >          painCave.severity = OPENMD_WARNING;
340 >          simError();
341 >        }
342 >      }
343 >      rSwitch_ = rCut_;
344 >    }
345      
346      // Default to cubic switching function.
347      sft_ = cubic;
# Line 263 | Line 368 | namespace OpenMD {
368      }
369      switcher_->setSwitchType(sft_);
370      switcher_->setSwitch(rSwitch_, rCut_);
371 +    interactionMan_->setSwitchingRadius(rSwitch_);
372    }
373 +
374 +
375 +
376    
377    void ForceManager::initialize() {
378  
379      if (!info_->isTopologyDone()) {
380 +
381        info_->update();
382        interactionMan_->setSimInfo(info_);
383        interactionMan_->initialize();
# Line 275 | Line 385 | namespace OpenMD {
385        // We want to delay the cutoffs until after the interaction
386        // manager has set up the atom-atom interactions so that we can
387        // query them for suggested cutoff values
278 –
388        setupCutoffs();
280 –      setupSwitching();
389  
390        info_->prepareTopology();      
391 +
392 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 +  
394      }
395  
396      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
397      
398 <    // Force fields can set options on how to scale van der Waals and electrostatic
399 <    // interactions for atoms connected via bonds, bends and torsions
400 <    // in this case the topological distance between atoms is:
398 >    // Force fields can set options on how to scale van der Waals and
399 >    // electrostatic interactions for atoms connected via bonds, bends
400 >    // and torsions in this case the topological distance between
401 >    // atoms is:
402      // 0 = topologically unconnected
403      // 1 = bonded together
404      // 2 = connected via a bend
# Line 338 | Line 450 | namespace OpenMD {
450      
451      for (mol = info_->beginMolecule(mi); mol != NULL;
452           mol = info_->nextMolecule(mi)) {
453 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
453 >      for(atom = mol->beginAtom(ai); atom != NULL;
454 >          atom = mol->nextAtom(ai)) {
455          atom->zeroForcesAndTorques();
456        }
457 <          
457 >      
458        //change the positions of atoms which belong to the rigidbodies
459        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
460             rb = mol->nextRigidBody(rbIter)) {
461          rb->zeroForcesAndTorques();
462        }        
463 <
463 >      
464        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
465          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
466              cg = mol->nextCutoffGroup(ci)) {
# Line 356 | Line 469 | namespace OpenMD {
469          }
470        }      
471      }
472 <  
472 >    
473      // Zero out the stress tensor
474      tau *= 0.0;
475      
# Line 392 | Line 505 | namespace OpenMD {
505  
506        for (bond = mol->beginBond(bondIter); bond != NULL;
507             bond = mol->nextBond(bondIter)) {
508 <        bond->calcForce();
508 >        bond->calcForce(doParticlePot_);
509          bondPotential += bond->getPotential();
510        }
511  
# Line 400 | Line 513 | namespace OpenMD {
513             bend = mol->nextBend(bendIter)) {
514          
515          RealType angle;
516 <        bend->calcForce(angle);
516 >        bend->calcForce(angle, doParticlePot_);
517          RealType currBendPot = bend->getPotential();          
518          
519          bendPotential += bend->getPotential();
# Line 410 | Line 523 | namespace OpenMD {
523            dataSet.prev.angle = dataSet.curr.angle = angle;
524            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
525            dataSet.deltaV = 0.0;
526 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
526 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
527 >                                                                  dataSet));
528          }else {
529            i->second.prev.angle = i->second.curr.angle;
530            i->second.prev.potential = i->second.curr.potential;
# Line 424 | Line 538 | namespace OpenMD {
538        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
539             torsion = mol->nextTorsion(torsionIter)) {
540          RealType angle;
541 <        torsion->calcForce(angle);
541 >        torsion->calcForce(angle, doParticlePot_);
542          RealType currTorsionPot = torsion->getPotential();
543          torsionPotential += torsion->getPotential();
544          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 448 | Line 562 | namespace OpenMD {
562             inversion != NULL;
563             inversion = mol->nextInversion(inversionIter)) {
564          RealType angle;
565 <        inversion->calcForce(angle);
565 >        inversion->calcForce(angle, doParticlePot_);
566          RealType currInversionPot = inversion->getPotential();
567          inversionPotential += inversion->getPotential();
568          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 527 | Line 641 | namespace OpenMD {
641      RealType vpair;
642      potVec longRangePotential(0.0);
643      potVec workPot(0.0);
644 +    vector<int>::iterator ia, jb;
645  
646      int loopStart, loopEnd;
647  
# Line 539 | Line 654 | namespace OpenMD {
654      idat.sw = &sw;
655      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
656      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
657 +    idat.doParticlePot = doParticlePot_;
658 +    sdat.doParticlePot = doParticlePot_;
659      
660      loopEnd = PAIR_LOOP;
661      if (info_->requiresPrepair() ) {
# Line 553 | Line 670 | namespace OpenMD {
670          bool update_nlist = fDecomp_->checkNeighborList();
671          if (update_nlist)
672            neighborList = fDecomp_->buildNeighborList();
673 <      }      
674 <        
673 >      }            
674 >
675        for (vector<pair<int, int> >::iterator it = neighborList.begin();
676               it != neighborList.end(); ++it) {
677                  
# Line 564 | Line 681 | namespace OpenMD {
681          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
682  
683          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
684 +
685          curSnapshot->wrapVector(d_grp);        
686          rgrpsq = d_grp.lengthSquare();
569 –
687          rCutSq = cuts.second;
688  
689          if (rgrpsq < rCutSq) {
690            idat.rcut = &cuts.first;
691            if (iLoop == PAIR_LOOP) {
692 <            vij *= 0.0;
692 >            vij = 0.0;
693              fij = V3Zero;
694            }
695            
696            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
697                                                       rgrp);
698 <              
698 >          
699            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
700            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
701  
702 <          for (vector<int>::iterator ia = atomListRow.begin();
702 >          for (ia = atomListRow.begin();
703                 ia != atomListRow.end(); ++ia) {            
704              atom1 = (*ia);
705              
706 <            for (vector<int>::iterator jb = atomListColumn.begin();
706 >            for (jb = atomListColumn.begin();
707                   jb != atomListColumn.end(); ++jb) {              
708                atom2 = (*jb);
709 <            
709 >
710                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
711                  vpair = 0.0;
712                  workPot = 0.0;
# Line 611 | Line 728 | namespace OpenMD {
728                    idat.d = &d;
729                    idat.r2 = &r2;
730                  }
731 <                
731 >              
732                  r = sqrt( *(idat.r2) );
733                  idat.rij = &r;
734                
# Line 632 | Line 749 | namespace OpenMD {
749              if (in_switching_region) {
750                swderiv = vij * dswdr / rgrp;
751                fg = swderiv * d_grp;
635 –
752                fij += fg;
753  
754                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
755                  tau -= outProduct( *(idat.d), fg);
756                }
757            
758 <              for (vector<int>::iterator ia = atomListRow.begin();
758 >              for (ia = atomListRow.begin();
759                     ia != atomListRow.end(); ++ia) {            
760                  atom1 = (*ia);                
761                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 647 | Line 763 | namespace OpenMD {
763                  // presence in switching region
764                  fg = swderiv * d_grp * mf;
765                  fDecomp_->addForceToAtomRow(atom1, fg);
650 –
766                  if (atomListRow.size() > 1) {
767                    if (info_->usesAtomicVirial()) {
768                      // find the distance between the atom
# Line 657 | Line 772 | namespace OpenMD {
772                    }
773                  }
774                }
775 <              for (vector<int>::iterator jb = atomListColumn.begin();
775 >              for (jb = atomListColumn.begin();
776                     jb != atomListColumn.end(); ++jb) {              
777                  atom2 = (*jb);
778                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 676 | Line 791 | namespace OpenMD {
791                  }
792                }
793              }
794 <            //if (!SIM_uses_AtomicVirial) {
794 >            //if (!info_->usesAtomicVirial()) {
795              //  tau -= outProduct(d_grp, fij);
796              //}
797            }
# Line 684 | Line 799 | namespace OpenMD {
799        }
800  
801        if (iLoop == PREPAIR_LOOP) {
802 <        if (info_->requiresPrepair()) {            
802 >        if (info_->requiresPrepair()) {
803 >
804            fDecomp_->collectIntermediateData();
805  
806            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
807              fDecomp_->fillSelfData(sdat, atom1);
808              interactionMan_->doPreForce(sdat);
809            }
694 –          
695 –          
696 –          fDecomp_->distributeIntermediateData();        
697 –        }
698 –      }
810  
811 <    }
701 <    
702 <    fDecomp_->collectData();
703 <    
704 <    if ( info_->requiresSkipCorrection() ) {
705 <      
706 <      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
811 >          fDecomp_->distributeIntermediateData();
812  
708 –        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
709 –        
710 –        for (vector<int>::iterator jb = skipList.begin();
711 –             jb != skipList.end(); ++jb) {        
712 –    
713 –          atom2 = (*jb);
714 –          fDecomp_->fillSkipData(idat, atom1, atom2);
715 –          interactionMan_->doSkipCorrection(idat);
716 –          fDecomp_->unpackSkipData(idat, atom1, atom2);
717 –
813          }
814        }
815      }
816      
817 +    fDecomp_->collectData();
818 +        
819      if (info_->requiresSelfCorrection()) {
820  
821        for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
# Line 763 | Line 860 | namespace OpenMD {
860      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
861                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
862   #endif
863 <    curSnapshot->statData.setTau(tau);
863 >    curSnapshot->setTau(tau);
864    }
865  
866   } //end namespace OpenMD

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