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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

# Line 47 | Line 47
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
53   #define __OPENMD_C
# Line 62 | Line 63 | namespace OpenMD {
63   namespace OpenMD {
64    
65    ForceManager::ForceManager(SimInfo * info) : info_(info) {
66 <
67 < #ifdef IS_MPI
68 <    fDecomp_ = new ForceMatrixDecomposition(info_);
68 < #else
69 <    // fDecomp_ = new ForceSerialDecomposition(info);
70 < #endif
66 >    forceField_ = info_->getForceField();
67 >    interactionMan_ = new InteractionManager();
68 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
69    }
70 +
71 +  /**
72 +   * setupCutoffs
73 +   *
74 +   * Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
75 +   *
76 +   * cutoffRadius : realType
77 +   *  If the cutoffRadius was explicitly set, use that value.
78 +   *  If the cutoffRadius was not explicitly set:
79 +   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
80 +   *      No electrostatic atoms?  Poll the atom types present in the
81 +   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
82 +   *      Use the maximum suggested value that was found.
83 +   *
84 +   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
85 +   *      If cutoffMethod was explicitly set, use that choice.
86 +   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
87 +   *
88 +   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
89 +   *      If cutoffPolicy was explicitly set, use that choice.
90 +   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
91 +   */
92 +  void ForceManager::setupCutoffs() {
93 +    
94 +    Globals* simParams_ = info_->getSimParams();
95 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
96 +    
97 +    if (simParams_->haveCutoffRadius()) {
98 +      rCut_ = simParams_->getCutoffRadius();
99 +    } else {      
100 +      if (info_->usesElectrostaticAtoms()) {
101 +        sprintf(painCave.errMsg,
102 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
103 +                "\tOpenMD will use a default value of 12.0 angstroms"
104 +                "\tfor the cutoffRadius.\n");
105 +        painCave.isFatal = 0;
106 +        painCave.severity = OPENMD_INFO;
107 +        simError();
108 +        rCut_ = 12.0;
109 +      } else {
110 +        RealType thisCut;
111 +        set<AtomType*>::iterator i;
112 +        set<AtomType*> atomTypes;
113 +        atomTypes = info_->getSimulatedAtomTypes();        
114 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
115 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
116 +          rCut_ = max(thisCut, rCut_);
117 +        }
118 +        sprintf(painCave.errMsg,
119 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
120 +                "\tOpenMD will use %lf angstroms.\n",
121 +                rCut_);
122 +        painCave.isFatal = 0;
123 +        painCave.severity = OPENMD_INFO;
124 +        simError();
125 +      }
126 +      fDecomp_->setUserCutoff(rCut_);
127 +    }
128 +
129 +    map<string, CutoffMethod> stringToCutoffMethod;
130 +    stringToCutoffMethod["HARD"] = HARD;
131 +    stringToCutoffMethod["SWITCHED"] = SWITCHED;
132 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
133 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
134    
135 <  void ForceManager::calcForces() {
135 >    if (simParams_->haveCutoffMethod()) {
136 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
137 >      map<string, CutoffMethod>::iterator i;
138 >      i = stringToCutoffMethod.find(cutMeth);
139 >      if (i == stringToCutoffMethod.end()) {
140 >        sprintf(painCave.errMsg,
141 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
142 >                "\tShould be one of: "
143 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
144 >                cutMeth.c_str());
145 >        painCave.isFatal = 1;
146 >        painCave.severity = OPENMD_ERROR;
147 >        simError();
148 >      } else {
149 >        cutoffMethod_ = i->second;
150 >      }
151 >    } else {
152 >      sprintf(painCave.errMsg,
153 >              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
154 >              "\tOpenMD will use SHIFTED_FORCE.\n");
155 >      painCave.isFatal = 0;
156 >      painCave.severity = OPENMD_INFO;
157 >      simError();
158 >      cutoffMethod_ = SHIFTED_FORCE;        
159 >    }
160 >
161 >    map<string, CutoffPolicy> stringToCutoffPolicy;
162 >    stringToCutoffPolicy["MIX"] = MIX;
163 >    stringToCutoffPolicy["MAX"] = MAX;
164 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
165 >
166 >    std::string cutPolicy;
167 >    if (forceFieldOptions_.haveCutoffPolicy()){
168 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
169 >    }else if (simParams_->haveCutoffPolicy()) {
170 >      cutPolicy = simParams_->getCutoffPolicy();
171 >    }
172 >
173 >    if (!cutPolicy.empty()){
174 >      toUpper(cutPolicy);
175 >      map<string, CutoffPolicy>::iterator i;
176 >      i = stringToCutoffPolicy.find(cutPolicy);
177 >
178 >      if (i == stringToCutoffPolicy.end()) {
179 >        sprintf(painCave.errMsg,
180 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
181 >                "\tShould be one of: "
182 >                "MIX, MAX, or TRADITIONAL\n",
183 >                cutPolicy.c_str());
184 >        painCave.isFatal = 1;
185 >        painCave.severity = OPENMD_ERROR;
186 >        simError();
187 >      } else {
188 >        cutoffPolicy_ = i->second;
189 >      }
190 >    } else {
191 >      sprintf(painCave.errMsg,
192 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
193 >              "\tOpenMD will use TRADITIONAL.\n");
194 >      painCave.isFatal = 0;
195 >      painCave.severity = OPENMD_INFO;
196 >      simError();
197 >      cutoffPolicy_ = TRADITIONAL;        
198 >    }
199 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
200 >  }
201 >
202 >  /**
203 >   * setupSwitching
204 >   *
205 >   * Sets the values of switchingRadius and
206 >   *  If the switchingRadius was explicitly set, use that value (but check it)
207 >   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
208 >   */
209 >  void ForceManager::setupSwitching() {
210 >    Globals* simParams_ = info_->getSimParams();
211 >
212 >    // create the switching function object:
213 >    switcher_ = new SwitchingFunction();
214      
215 +    if (simParams_->haveSwitchingRadius()) {
216 +      rSwitch_ = simParams_->getSwitchingRadius();
217 +      if (rSwitch_ > rCut_) {        
218 +        sprintf(painCave.errMsg,
219 +                "ForceManager::setupSwitching: switchingRadius (%f) is larger "
220 +                "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
221 +        painCave.isFatal = 1;
222 +        painCave.severity = OPENMD_ERROR;
223 +        simError();
224 +      }
225 +    } else {      
226 +      rSwitch_ = 0.85 * rCut_;
227 +      sprintf(painCave.errMsg,
228 +              "ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
229 +              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
230 +              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
231 +      painCave.isFatal = 0;
232 +      painCave.severity = OPENMD_WARNING;
233 +      simError();
234 +    }          
235 +    
236 +    // Default to cubic switching function.
237 +    sft_ = cubic;
238 +    if (simParams_->haveSwitchingFunctionType()) {
239 +      string funcType = simParams_->getSwitchingFunctionType();
240 +      toUpper(funcType);
241 +      if (funcType == "CUBIC") {
242 +        sft_ = cubic;
243 +      } else {
244 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
245 +          sft_ = fifth_order_poly;
246 +        } else {
247 +          // throw error        
248 +          sprintf( painCave.errMsg,
249 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
250 +                   "\tswitchingFunctionType must be one of: "
251 +                   "\"cubic\" or \"fifth_order_polynomial\".",
252 +                   funcType.c_str() );
253 +          painCave.isFatal = 1;
254 +          painCave.severity = OPENMD_ERROR;
255 +          simError();
256 +        }          
257 +      }
258 +    }
259 +    switcher_->setSwitchType(sft_);
260 +    switcher_->setSwitch(rSwitch_, rCut_);
261 +  }
262 +  
263 +  void ForceManager::initialize() {
264 +
265      if (!info_->isTopologyDone()) {
266        info_->update();
267        interactionMan_->setSimInfo(info_);
268        interactionMan_->initialize();
269 <      swfun_ = interactionMan_->getSwitchingFunction();
270 <      fDecomp_->distributeInitialData();
271 <      info_->prepareTopology();
269 >
270 >      // We want to delay the cutoffs until after the interaction
271 >      // manager has set up the atom-atom interactions so that we can
272 >      // query them for suggested cutoff values
273 >
274 >      setupCutoffs();
275 >      setupSwitching();
276 >
277 >      info_->prepareTopology();      
278      }
279 +
280 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
281      
282 +    // Force fields can set options on how to scale van der Waals and electrostatic
283 +    // interactions for atoms connected via bonds, bends and torsions
284 +    // in this case the topological distance between atoms is:
285 +    // 0 = topologically unconnected
286 +    // 1 = bonded together
287 +    // 2 = connected via a bend
288 +    // 3 = connected via a torsion
289 +    
290 +    vdwScale_.reserve(4);
291 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
292 +
293 +    electrostaticScale_.reserve(4);
294 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
295 +
296 +    vdwScale_[0] = 1.0;
297 +    vdwScale_[1] = fopts.getvdw12scale();
298 +    vdwScale_[2] = fopts.getvdw13scale();
299 +    vdwScale_[3] = fopts.getvdw14scale();
300 +    
301 +    electrostaticScale_[0] = 1.0;
302 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
303 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
304 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
305 +    
306 +    fDecomp_->distributeInitialData();
307 +
308 +    initialized_ = true;
309 +
310 +  }
311 +
312 +  void ForceManager::calcForces() {
313 +    
314 +    if (!initialized_) initialize();
315 +
316      preCalculation();  
317      shortRangeInteractions();
318      longRangeInteractions();
319 <    postCalculation();
88 <    
319 >    postCalculation();    
320    }
321    
322    void ForceManager::preCalculation() {
# Line 245 | Line 476 | namespace OpenMD {
476    
477    void ForceManager::longRangeInteractions() {
478  
248 –    // some of this initial stuff will go away:
479      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
480      DataStorage* config = &(curSnapshot->atomData);
481      DataStorage* cgConfig = &(curSnapshot->cgData);
252 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258 –    RealType* rc;    
482  
483 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
484 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
483 >    //calculate the center of mass of cutoff group
484 >
485 >    SimInfo::MoleculeIterator mi;
486 >    Molecule* mol;
487 >    Molecule::CutoffGroupIterator ci;
488 >    CutoffGroup* cg;
489 >
490 >    if(info_->getNCutoffGroups() > 0){      
491 >      for (mol = info_->beginMolecule(mi); mol != NULL;
492 >           mol = info_->nextMolecule(mi)) {
493 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494 >            cg = mol->nextCutoffGroup(ci)) {
495 >          cg->updateCOM();
496 >        }
497 >      }      
498      } else {
499        // center of mass of the group is the same as position of the atom  
500        // if cutoff group does not exist
501 <      rc = pos;
501 >      cgConfig->position = config->position;
502      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
503  
504 <    // dangerous to iterate over enums, but we'll live on the edge:
274 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275 <      longRangePotential[i]=0.0; //Initialize array
276 <    }
277 <
278 <    // new stuff starts here:
279 <
504 >    fDecomp_->zeroWorkArrays();
505      fDecomp_->distributeData();
506 <
507 <    int cg1, cg2, atom1, atom2;
508 <    Vector3d d_grp, dag;
509 <    RealType rgrpsq, rgrp;
506 >    
507 >    int cg1, cg2, atom1, atom2, topoDist;
508 >    Vector3d d_grp, dag, d;
509 >    RealType rgrpsq, rgrp, r2, r;
510 >    RealType electroMult, vdwMult;
511      RealType vij;
512 <    Vector3d fij, fg;
513 <    pair<int, int> gtypes;
512 >    Vector3d fij, fg, f1;
513 >    tuple3<RealType, RealType, RealType> cuts;
514      RealType rCutSq;
515      bool in_switching_region;
516      RealType sw, dswdr, swderiv;
# Line 292 | Line 518 | namespace OpenMD {
518      InteractionData idat;
519      SelfData sdat;
520      RealType mf;
521 +    potVec pot(0.0);
522 +    potVec longRangePotential(0.0);
523 +    RealType lrPot;
524 +    RealType vpair;
525  
526      int loopStart, loopEnd;
527  
528 +    idat.vdwMult = &vdwMult;
529 +    idat.electroMult = &electroMult;
530 +    idat.pot = &pot;
531 +    idat.vpair = &vpair;
532 +    idat.f1 = &f1;
533 +    idat.sw = &sw;
534 +
535      loopEnd = PAIR_LOOP;
536      if (info_->requiresPrepair() ) {
537        loopStart = PREPAIR_LOOP;
538      } else {
539        loopStart = PAIR_LOOP;
540      }
541 <
542 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
543 <      
541 >    
542 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
543 >    
544        if (iLoop == loopStart) {
545          bool update_nlist = fDecomp_->checkNeighborList();
546          if (update_nlist)
547            neighborList = fDecomp_->buildNeighborList();
548 <      }
549 <
548 >      }      
549 >        
550        for (vector<pair<int, int> >::iterator it = neighborList.begin();
551               it != neighborList.end(); ++it) {
552 <        
552 >                
553          cg1 = (*it).first;
554          cg2 = (*it).second;
555 +        
556 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
557  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
558          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
559          curSnapshot->wrapVector(d_grp);        
560          rgrpsq = d_grp.lengthSquare();
323 –        rCutSq = groupCutoffMap[gtypes].first;
561  
562 +        rCutSq = cuts.second;
563 +
564          if (rgrpsq < rCutSq) {
565 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
565 >          idat.rcut = &cuts.first;
566            if (iLoop == PAIR_LOOP) {
567              vij *= 0.0;
568              fij = V3Zero;
569            }
570            
571 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
572 <                                                  rgrp);              
571 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
572 >                                                     rgrp);
573 >              
574            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
575            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
576  
# Line 344 | Line 584 | namespace OpenMD {
584                
585                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
586                  
587 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
587 >                vpair = 0.0;
588 >                f1 = V3Zero;
589  
590 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
591 +                
592 +                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
593 +                vdwMult = vdwScale_[topoDist];
594 +                electroMult = electrostaticScale_[topoDist];
595 +
596                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
597 <                  *(idat.d) = d_grp;
598 <                  *(idat.r2) = rgrpsq;
597 >                  idat.d = &d_grp;
598 >                  idat.r2 = &rgrpsq;
599                  } else {
600 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
601 <                  curSnapshot->wrapVector( *(idat.d) );
602 <                  *(idat.r2) = idat.d->lengthSquare();
600 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
601 >                  curSnapshot->wrapVector( d );
602 >                  r2 = d.lengthSquare();
603 >                  idat.d = &d;
604 >                  idat.r2 = &r2;
605                  }
606                  
607 <                *(idat.rij) = sqrt( *(idat.r2) );
607 >                r = sqrt( *(idat.r2) );
608 >                idat.rij = &r;
609                
610                  if (iLoop == PREPAIR_LOOP) {
611                    interactionMan_->doPrePair(idat);
612                  } else {
613                    interactionMan_->doPair(idat);
614 <                  vij += *(idat.vpair);
615 <                  fij += *(idat.f1);
616 <                  tau -= outProduct( *(idat.d), *(idat.f1));
614 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
615 >                  vij += vpair;
616 >                  fij += f1;
617 >                  tau -= outProduct( *(idat.d), f1);
618                  }
619                }
620              }
# Line 427 | Line 678 | namespace OpenMD {
678        if (iLoop == PREPAIR_LOOP) {
679          if (info_->requiresPrepair()) {            
680            fDecomp_->collectIntermediateData();
681 <          atomListLocal = fDecomp_->getAtomList();
682 <          for (vector<int>::iterator ia = atomListLocal.begin();
683 <               ia != atomListLocal.end(); ++ia) {              
433 <            atom1 = (*ia);            
434 <            sdat = fDecomp_->fillSelfData(atom1);
681 >
682 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
683 >            fDecomp_->fillSelfData(sdat, atom1);
684              interactionMan_->doPreForce(sdat);
685            }
686 +
687            fDecomp_->distributeIntermediateData();        
688          }
689        }
# Line 442 | Line 692 | namespace OpenMD {
692      
693      fDecomp_->collectData();
694      
695 <    if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
696 <      atomListLocal = fDecomp_->getAtomList();
697 <      for (vector<int>::iterator ia = atomListLocal.begin();
448 <           ia != atomListLocal.end(); ++ia) {              
449 <        atom1 = (*ia);    
695 >    if ( info_->requiresSkipCorrection() ) {
696 >      
697 >      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
698  
699 <        if (info_->requiresSkipCorrection()) {
700 <          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
701 <          for (vector<int>::iterator jb = skipList.begin();
702 <               jb != skipList.end(); ++jb) {              
703 <            atom2 = (*jb);
704 <            idat = fDecomp_->fillSkipData(atom1, atom2);
705 <            interactionMan_->doSkipCorrection(idat);
706 <          }
699 >        vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
700 >        
701 >        for (vector<int>::iterator jb = skipList.begin();
702 >             jb != skipList.end(); ++jb) {        
703 >    
704 >          atom2 = (*jb);
705 >          fDecomp_->fillSkipData(idat, atom1, atom2);
706 >          interactionMan_->doSkipCorrection(idat);
707 >
708          }
460 –          
461 –        if (info_->requiresSelfCorrection()) {
462 –          sdat = fDecomp_->fillSelfData(atom1);
463 –          interactionMan_->doSelfCorrection(sdat);
464 –        }
709        }
710      }
711 +    
712 +    if (info_->requiresSelfCorrection()) {
713  
714 <    // dangerous to iterate over enums, but we'll live on the edge:
715 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
716 <      lrPot += longRangePotential[i]; //Quick hack
714 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
715 >        fDecomp_->fillSelfData(sdat, atom1);
716 >        interactionMan_->doSelfCorrection(sdat);
717 >      }
718 >
719      }
720 <        
720 >
721 >    longRangePotential = fDecomp_->getLongRangePotential();
722 >    lrPot = longRangePotential.sum();
723 >
724      //store the tau and long range potential    
725      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
726      curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];

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