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Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 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 86 | 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     *
# Line 107 | Line 109 | namespace OpenMD {
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 165 | 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 179 | 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 241 | Line 318 | namespace OpenMD {
318          simError();
319        }
320      } else {
321 <      if (simParams_->haveSwitchingRadius()) {
322 <        map<string, CutoffMethod>::const_iterator it;
323 <        string theMeth;
324 <        for (it = stringToCutoffMethod.begin();
325 <             it != stringToCutoffMethod.end(); ++it) {
326 <          if (it->second == cutoffMethod_) {
327 <            theMeth = it->first;
328 <            break;
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          }
254 –        sprintf(painCave.errMsg,
255 –                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
256 –                "\tis not set to SWITCHED, so switchingRadius value\n"
257 –                "\twill be ignored for this simulation\n", theMeth.c_str());
258 –        painCave.isFatal = 0;
259 –        painCave.severity = OPENMD_WARNING;
260 –        simError();
342        }
262 –
343        rSwitch_ = rCut_;
344      }
345      
# Line 290 | Line 370 | namespace OpenMD {
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 301 | 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
304 –
388        setupCutoffs();
389  
390        info_->prepareTopology();      
# Line 309 | Line 392 | namespace OpenMD {
392  
393      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
394      
395 <    // Force fields can set options on how to scale van der Waals and electrostatic
396 <    // interactions for atoms connected via bonds, bends and torsions
397 <    // in this case the topological distance between atoms is:
395 >    // Force fields can set options on how to scale van der Waals and
396 >    // electrostatic interactions for atoms connected via bonds, bends
397 >    // and torsions in this case the topological distance between
398 >    // atoms is:
399      // 0 = topologically unconnected
400      // 1 = bonded together
401      // 2 = connected via a bend
# Line 363 | Line 447 | namespace OpenMD {
447      
448      for (mol = info_->beginMolecule(mi); mol != NULL;
449           mol = info_->nextMolecule(mi)) {
450 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
450 >      for(atom = mol->beginAtom(ai); atom != NULL;
451 >          atom = mol->nextAtom(ai)) {
452          atom->zeroForcesAndTorques();
453        }
454 <          
454 >      
455        //change the positions of atoms which belong to the rigidbodies
456        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
457             rb = mol->nextRigidBody(rbIter)) {
458          rb->zeroForcesAndTorques();
459        }        
460 <
460 >      
461        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
462          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
463              cg = mol->nextCutoffGroup(ci)) {
# Line 381 | Line 466 | namespace OpenMD {
466          }
467        }      
468      }
469 <  
469 >    
470      // Zero out the stress tensor
471      tau *= 0.0;
472      
# Line 435 | Line 520 | namespace OpenMD {
520            dataSet.prev.angle = dataSet.curr.angle = angle;
521            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
522            dataSet.deltaV = 0.0;
523 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
523 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
524 >                                                                  dataSet));
525          }else {
526            i->second.prev.angle = i->second.curr.angle;
527            i->second.prev.potential = i->second.curr.potential;
# Line 578 | Line 664 | namespace OpenMD {
664          bool update_nlist = fDecomp_->checkNeighborList();
665          if (update_nlist)
666            neighborList = fDecomp_->buildNeighborList();
667 <      }      
668 <        
667 >      }            
668 >
669        for (vector<pair<int, int> >::iterator it = neighborList.begin();
670               it != neighborList.end(); ++it) {
671                  
# Line 589 | Line 675 | namespace OpenMD {
675          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
676  
677          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
678 +
679          curSnapshot->wrapVector(d_grp);        
680          rgrpsq = d_grp.lengthSquare();
594 –
681          rCutSq = cuts.second;
682  
683          if (rgrpsq < rCutSq) {
# Line 603 | Line 689 | namespace OpenMD {
689            
690            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
691                                                       rgrp);
692 <              
692 >          
693            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
694            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
695  
# Line 614 | Line 700 | namespace OpenMD {
700              for (vector<int>::iterator jb = atomListColumn.begin();
701                   jb != atomListColumn.end(); ++jb) {              
702                atom2 = (*jb);
703 <            
703 >
704                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
705                  vpair = 0.0;
706                  workPot = 0.0;
# Line 636 | Line 722 | namespace OpenMD {
722                    idat.d = &d;
723                    idat.r2 = &r2;
724                  }
725 <                
725 >              
726                  r = sqrt( *(idat.r2) );
727                  idat.rij = &r;
728                
# Line 671 | Line 757 | namespace OpenMD {
757                  // presence in switching region
758                  fg = swderiv * d_grp * mf;
759                  fDecomp_->addForceToAtomRow(atom1, fg);
674 –
760                  if (atomListRow.size() > 1) {
761                    if (info_->usesAtomicVirial()) {
762                      // find the distance between the atom
# Line 700 | Line 785 | namespace OpenMD {
785                  }
786                }
787              }
788 <            //if (!SIM_uses_AtomicVirial) {
788 >            //if (!info_->usesAtomicVirial()) {
789              //  tau -= outProduct(d_grp, fij);
790              //}
791            }
# Line 708 | Line 793 | namespace OpenMD {
793        }
794  
795        if (iLoop == PREPAIR_LOOP) {
796 <        if (info_->requiresPrepair()) {            
796 >        if (info_->requiresPrepair()) {
797 >
798            fDecomp_->collectIntermediateData();
799  
800            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
801              fDecomp_->fillSelfData(sdat, atom1);
802              interactionMan_->doPreForce(sdat);
803            }
804 <          
805 <          
806 <          fDecomp_->distributeIntermediateData();        
804 >
805 >          fDecomp_->distributeIntermediateData();
806 >
807          }
808        }
723 –
809      }
810      
811      fDecomp_->collectData();
# Line 769 | Line 854 | namespace OpenMD {
854      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
856   #endif
857 <    curSnapshot->statData.setTau(tau);
857 >    curSnapshot->setTau(tau);
858    }
859  
860   } //end namespace OpenMD

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