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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

# Line 86 | Line 86 | namespace OpenMD {
86     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87     *      Use the maximum suggested value that was found.
88     *
89 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90 >   *                        or SHIFTED_POTENTIAL)
91     *      If cutoffMethod was explicitly set, use that choice.
92     *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93     *
# Line 107 | Line 108 | namespace OpenMD {
108      
109      Globals* simParams_ = info_->getSimParams();
110      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111 +    int mdFileVersion;
112      
113 +    if (simParams_->haveMDfileVersion())
114 +      mdFileVersion = simParams_->getMDfileVersion();
115 +    else
116 +      mdFileVersion = 0;
117 +  
118      if (simParams_->haveCutoffRadius()) {
119        rCut_ = simParams_->getCutoffRadius();
120      } else {      
# Line 165 | Line 172 | namespace OpenMD {
172          cutoffMethod_ = i->second;
173        }
174      } else {
175 <      sprintf(painCave.errMsg,
176 <              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
177 <              "\tOpenMD will use SHIFTED_FORCE.\n");
178 <      painCave.isFatal = 0;
179 <      painCave.severity = OPENMD_INFO;
180 <      simError();
181 <      cutoffMethod_ = SHIFTED_FORCE;        
175 >      if (mdFileVersion > 1) {
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;        
183 >      } else {
184 >        // handle the case where the old file version was in play
185 >        // (there should be no cutoffMethod, so we have to deduce it
186 >        // from other data).        
187 >
188 >        sprintf(painCave.errMsg,
189 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
190 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
191 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
192 >                "\tbehavior of the older (version 1) code.  To remove this\n"
193 >                "\twarning, add an explicit cutoffMethod and change the top\n"
194 >                "\tof the file so that it begins with <OpenMD version=2>\n");
195 >        painCave.isFatal = 0;
196 >        painCave.severity = OPENMD_WARNING;
197 >        simError();            
198 >                
199 >        // The old file version tethered the shifting behavior to the
200 >        // electrostaticSummationMethod keyword.
201 >        
202 >        if (simParams_->haveElectrostaticSummationMethod()) {
203 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
204 >          toUpper(myMethod);
205 >        
206 >          if (myMethod == "SHIFTED_POTENTIAL") {
207 >            cutoffMethod_ = SHIFTED_POTENTIAL;
208 >          } else if (myMethod == "SHIFTED_FORCE") {
209 >            cutoffMethod_ = SHIFTED_FORCE;
210 >          }
211 >        
212 >          if (simParams_->haveSwitchingRadius())
213 >            rSwitch_ = simParams_->getSwitchingRadius();
214 >
215 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
216 >            if (simParams_->haveSwitchingRadius()){
217 >              sprintf(painCave.errMsg,
218 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
219 >                      "\tA value was set for the switchingRadius\n"
220 >                      "\teven though the electrostaticSummationMethod was\n"
221 >                      "\tset to %s\n", myMethod.c_str());
222 >              painCave.severity = OPENMD_WARNING;
223 >              painCave.isFatal = 1;
224 >              simError();            
225 >            }
226 >          }
227 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
228 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
229 >              sprintf(painCave.errMsg,
230 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
231 >                      "\tcutoffRadius and switchingRadius are set to the\n"
232 >                      "\tsame value.  OpenMD will use shifted force\n"
233 >                      "\tpotentials instead of switching functions.\n");
234 >              painCave.isFatal = 0;
235 >              painCave.severity = OPENMD_WARNING;
236 >              simError();            
237 >            } else {
238 >              cutoffMethod_ = SHIFTED_POTENTIAL;
239 >              sprintf(painCave.errMsg,
240 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
241 >                      "\tcutoffRadius and switchingRadius are set to the\n"
242 >                      "\tsame value.  OpenMD will use shifted potentials\n"
243 >                      "\tinstead of switching functions.\n");
244 >              painCave.isFatal = 0;
245 >              painCave.severity = OPENMD_WARNING;
246 >              simError();            
247 >            }
248 >          }
249 >        }
250 >      }
251      }
252  
253      map<string, CutoffPolicy> stringToCutoffPolicy;
# Line 290 | Line 366 | namespace OpenMD {
366      switcher_->setSwitch(rSwitch_, rCut_);
367      interactionMan_->setSwitchingRadius(rSwitch_);
368    }
369 +
370 +
371 +
372    
373    void ForceManager::initialize() {
374  
375      if (!info_->isTopologyDone()) {
376 +
377        info_->update();
378        interactionMan_->setSimInfo(info_);
379        interactionMan_->initialize();
# Line 301 | Line 381 | namespace OpenMD {
381        // We want to delay the cutoffs until after the interaction
382        // manager has set up the atom-atom interactions so that we can
383        // query them for suggested cutoff values
304 –
384        setupCutoffs();
385  
386        info_->prepareTopology();      
# Line 309 | Line 388 | namespace OpenMD {
388  
389      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
390      
391 <    // Force fields can set options on how to scale van der Waals and electrostatic
392 <    // interactions for atoms connected via bonds, bends and torsions
393 <    // in this case the topological distance between atoms is:
391 >    // Force fields can set options on how to scale van der Waals and
392 >    // electrostatic interactions for atoms connected via bonds, bends
393 >    // and torsions in this case the topological distance between
394 >    // atoms is:
395      // 0 = topologically unconnected
396      // 1 = bonded together
397      // 2 = connected via a bend
# Line 363 | Line 443 | namespace OpenMD {
443      
444      for (mol = info_->beginMolecule(mi); mol != NULL;
445           mol = info_->nextMolecule(mi)) {
446 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
446 >      for(atom = mol->beginAtom(ai); atom != NULL;
447 >          atom = mol->nextAtom(ai)) {
448          atom->zeroForcesAndTorques();
449        }
450 <          
450 >      
451        //change the positions of atoms which belong to the rigidbodies
452        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
453             rb = mol->nextRigidBody(rbIter)) {
454          rb->zeroForcesAndTorques();
455        }        
456 <
456 >      
457        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
458          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
459              cg = mol->nextCutoffGroup(ci)) {
# Line 381 | Line 462 | namespace OpenMD {
462          }
463        }      
464      }
465 <  
465 >    
466      // Zero out the stress tensor
467      tau *= 0.0;
468      
# Line 435 | Line 516 | namespace OpenMD {
516            dataSet.prev.angle = dataSet.curr.angle = angle;
517            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
518            dataSet.deltaV = 0.0;
519 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
519 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
520 >                                                                  dataSet));
521          }else {
522            i->second.prev.angle = i->second.curr.angle;
523            i->second.prev.potential = i->second.curr.potential;
# Line 578 | Line 660 | namespace OpenMD {
660          bool update_nlist = fDecomp_->checkNeighborList();
661          if (update_nlist)
662            neighborList = fDecomp_->buildNeighborList();
663 <      }      
664 <        
663 >      }            
664 >
665        for (vector<pair<int, int> >::iterator it = neighborList.begin();
666               it != neighborList.end(); ++it) {
667                  
# Line 589 | Line 671 | namespace OpenMD {
671          cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
672  
673          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
674 +
675          curSnapshot->wrapVector(d_grp);        
676          rgrpsq = d_grp.lengthSquare();
594 –
677          rCutSq = cuts.second;
678  
679          if (rgrpsq < rCutSq) {
# Line 603 | Line 685 | namespace OpenMD {
685            
686            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
687                                                       rgrp);
688 <              
688 >          
689            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
690            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
691  
# Line 614 | Line 696 | namespace OpenMD {
696              for (vector<int>::iterator jb = atomListColumn.begin();
697                   jb != atomListColumn.end(); ++jb) {              
698                atom2 = (*jb);
699 <            
699 >
700                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
701                  vpair = 0.0;
702                  workPot = 0.0;
# Line 636 | Line 718 | namespace OpenMD {
718                    idat.d = &d;
719                    idat.r2 = &r2;
720                  }
721 <                
721 >              
722                  r = sqrt( *(idat.r2) );
723                  idat.rij = &r;
724                
# Line 671 | Line 753 | namespace OpenMD {
753                  // presence in switching region
754                  fg = swderiv * d_grp * mf;
755                  fDecomp_->addForceToAtomRow(atom1, fg);
674 –
756                  if (atomListRow.size() > 1) {
757                    if (info_->usesAtomicVirial()) {
758                      // find the distance between the atom
# Line 700 | Line 781 | namespace OpenMD {
781                  }
782                }
783              }
784 <            //if (!SIM_uses_AtomicVirial) {
784 >            //if (!info_->usesAtomicVirial()) {
785              //  tau -= outProduct(d_grp, fij);
786              //}
787            }
# Line 708 | Line 789 | namespace OpenMD {
789        }
790  
791        if (iLoop == PREPAIR_LOOP) {
792 <        if (info_->requiresPrepair()) {            
792 >        if (info_->requiresPrepair()) {
793 >
794            fDecomp_->collectIntermediateData();
795  
796            for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
797              fDecomp_->fillSelfData(sdat, atom1);
798              interactionMan_->doPreForce(sdat);
799            }
800 <          
801 <          
802 <          fDecomp_->distributeIntermediateData();        
800 >
801 >          fDecomp_->distributeIntermediateData();
802 >
803          }
804        }
723 –
805      }
806      
807      fDecomp_->collectData();

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