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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
47   using namespace std;
48   namespace OpenMD {
# Line 54 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60      nGroups_ = snap_->getNumberOfCutoffGroups();
61  
62 +    // gather the information for atomtype IDs (atids):
63 +    identsLocal = info_->getIdentArray();
64 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 +    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 +    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 +    PairList excludes = info_->getExcludedInteractions();
69 +    PairList oneTwo = info_->getOneTwoInteractions();
70 +    PairList oneThree = info_->getOneThreeInteractions();
71 +    PairList oneFour = info_->getOneFourInteractions();
72 +    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
73 +
74   #ifdef IS_MPI
75  
76      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
# Line 93 | Line 107 | namespace OpenMD {
107                                        vector<RealType> (nAtomsInRow_, 0.0));
108      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
109                                        vector<RealType> (nAtomsInCol_, 0.0));
96 –
97 –
98 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
110      
100 –    // gather the information for atomtype IDs (atids):
101 –    vector<int> identsLocal = info_->getIdentArray();
111      identsRow.reserve(nAtomsInRow_);
112      identsCol.reserve(nAtomsInCol_);
113      
114      AtomCommIntRow->gather(identsLocal, identsRow);
115      AtomCommIntColumn->gather(identsLocal, identsCol);
116      
108 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
117      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
118      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
119      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
120      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
121      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
122  
123 <    // still need:
124 <    // topoDist
125 <    // exclude
123 >    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
124 >    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
125 >
126 >    groupListRow_.clear();
127 >    groupListRow_.reserve(nGroupsInRow_);
128 >    for (int i = 0; i < nGroupsInRow_; i++) {
129 >      int gid = cgRowToGlobal[i];
130 >      for (int j = 0; j < nAtomsInRow_; j++) {
131 >        int aid = AtomRowToGlobal[j];
132 >        if (globalGroupMembership[aid] == gid)
133 >          groupListRow_[i].push_back(j);
134 >      }      
135 >    }
136 >
137 >    groupListCol_.clear();
138 >    groupListCol_.reserve(nGroupsInCol_);
139 >    for (int i = 0; i < nGroupsInCol_; i++) {
140 >      int gid = cgColToGlobal[i];
141 >      for (int j = 0; j < nAtomsInCol_; j++) {
142 >        int aid = AtomColToGlobal[j];
143 >        if (globalGroupMembership[aid] == gid)
144 >          groupListCol_[i].push_back(j);
145 >      }      
146 >    }
147 >
148 >    skipsForRowAtom.clear();
149 >    skipsForRowAtom.reserve(nAtomsInRow_);
150 >    for (int i = 0; i < nAtomsInRow_; i++) {
151 >      int iglob = AtomRowToGlobal[i];
152 >      for (int j = 0; j < nAtomsInCol_; j++) {
153 >        int jglob = AtomColToGlobal[j];        
154 >        if (excludes.hasPair(iglob, jglob))
155 >          skipsForRowAtom[i].push_back(j);      
156 >      }      
157 >    }
158 >
159 >    toposForRowAtom.clear();
160 >    toposForRowAtom.reserve(nAtomsInRow_);
161 >    for (int i = 0; i < nAtomsInRow_; i++) {
162 >      int iglob = AtomRowToGlobal[i];
163 >      int nTopos = 0;
164 >      for (int j = 0; j < nAtomsInCol_; j++) {
165 >        int jglob = AtomColToGlobal[j];        
166 >        if (oneTwo.hasPair(iglob, jglob)) {
167 >          toposForRowAtom[i].push_back(j);
168 >          topoDistRow[i][nTopos] = 1;
169 >          nTopos++;
170 >        }
171 >        if (oneThree.hasPair(iglob, jglob)) {
172 >          toposForRowAtom[i].push_back(j);
173 >          topoDistRow[i][nTopos] = 2;
174 >          nTopos++;
175 >        }
176 >        if (oneFour.hasPair(iglob, jglob)) {
177 >          toposForRowAtom[i].push_back(j);
178 >          topoDistRow[i][nTopos] = 3;
179 >          nTopos++;
180 >        }
181 >      }      
182 >    }
183 >
184   #endif
120 –  }
121 –    
185  
186 +    groupList_.clear();
187 +    groupList_.reserve(nGroups_);
188 +    for (int i = 0; i < nGroups_; i++) {
189 +      int gid = cgLocalToGlobal[i];
190 +      for (int j = 0; j < nLocal_; j++) {
191 +        int aid = AtomLocalToGlobal[j];
192 +        if (globalGroupMembership[aid] == gid)
193 +          groupList_[i].push_back(j);
194 +      }      
195 +    }
196  
197 +    skipsForLocalAtom.clear();
198 +    skipsForLocalAtom.reserve(nLocal_);
199 +
200 +    for (int i = 0; i < nLocal_; i++) {
201 +      int iglob = AtomLocalToGlobal[i];
202 +      for (int j = 0; j < nLocal_; j++) {
203 +        int jglob = AtomLocalToGlobal[j];        
204 +        if (excludes.hasPair(iglob, jglob))
205 +          skipsForLocalAtom[i].push_back(j);      
206 +      }      
207 +    }
208 +
209 +    toposForLocalAtom.clear();
210 +    toposForLocalAtom.reserve(nLocal_);
211 +    for (int i = 0; i < nLocal_; i++) {
212 +      int iglob = AtomLocalToGlobal[i];
213 +      int nTopos = 0;
214 +      for (int j = 0; j < nLocal_; j++) {
215 +        int jglob = AtomLocalToGlobal[j];        
216 +        if (oneTwo.hasPair(iglob, jglob)) {
217 +          toposForLocalAtom[i].push_back(j);
218 +          topoDistLocal[i][nTopos] = 1;
219 +          nTopos++;
220 +        }
221 +        if (oneThree.hasPair(iglob, jglob)) {
222 +          toposForLocalAtom[i].push_back(j);
223 +          topoDistLocal[i][nTopos] = 2;
224 +          nTopos++;
225 +        }
226 +        if (oneFour.hasPair(iglob, jglob)) {
227 +          toposForLocalAtom[i].push_back(j);
228 +          topoDistLocal[i][nTopos] = 3;
229 +          nTopos++;
230 +        }
231 +      }      
232 +    }
233 +  }
234 +  
235    void ForceMatrixDecomposition::distributeData()  {
236      snap_ = sman_->getCurrentSnapshot();
237      storageLayout_ = sman_->getStorageLayout();
# Line 244 | Line 355 | namespace OpenMD {
355   #endif
356    }
357  
358 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
359 + #ifdef IS_MPI
360 +    return nAtomsInRow_;
361 + #else
362 +    return nLocal_;
363 + #endif
364 +  }
365 +
366 +  /**
367 +   * returns the list of atoms belonging to this group.  
368 +   */
369 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
370 + #ifdef IS_MPI
371 +    return groupListRow_[cg1];
372 + #else
373 +    return groupList_[cg1];
374 + #endif
375 +  }
376 +
377 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
378 + #ifdef IS_MPI
379 +    return groupListCol_[cg2];
380 + #else
381 +    return groupList_[cg2];
382 + #endif
383 +  }
384    
385    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
386      Vector3d d;
# Line 285 | Line 422 | namespace OpenMD {
422      snap_->wrapVector(d);
423      return d;    
424    }
425 +
426 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
427 + #ifdef IS_MPI
428 +    return massFactorsRow[atom1];
429 + #else
430 +    return massFactorsLocal[atom1];
431 + #endif
432 +  }
433 +
434 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
435 + #ifdef IS_MPI
436 +    return massFactorsCol[atom2];
437 + #else
438 +    return massFactorsLocal[atom2];
439 + #endif
440 +
441 +  }
442      
443    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
444      Vector3d d;
# Line 297 | Line 451 | namespace OpenMD {
451  
452      snap_->wrapVector(d);
453      return d;    
454 +  }
455 +
456 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
457 + #ifdef IS_MPI
458 +    return skipsForRowAtom[atom1];
459 + #else
460 +    return skipsForLocalAtom[atom1];
461 + #endif
462 +  }
463 +
464 +  /**
465 +   * there are a number of reasons to skip a pair or a particle mostly
466 +   * we do this to exclude atoms who are involved in short range
467 +   * interactions (bonds, bends, torsions), but we also need to
468 +   * exclude some overcounted interactions that result from the
469 +   * parallel decomposition.
470 +   */
471 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
472 +    int unique_id_1, unique_id_2;
473 +
474 + #ifdef IS_MPI
475 +    // in MPI, we have to look up the unique IDs for each atom
476 +    unique_id_1 = AtomRowToGlobal[atom1];
477 +    unique_id_2 = AtomColToGlobal[atom2];
478 +
479 +    // this situation should only arise in MPI simulations
480 +    if (unique_id_1 == unique_id_2) return true;
481 +    
482 +    // this prevents us from doing the pair on multiple processors
483 +    if (unique_id_1 < unique_id_2) {
484 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
485 +    } else {
486 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
487 +    }
488 + #else
489 +    // in the normal loop, the atom numbers are unique
490 +    unique_id_1 = atom1;
491 +    unique_id_2 = atom2;
492 + #endif
493 +    
494 + #ifdef IS_MPI
495 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
496 +         i != skipsForRowAtom[atom1].end(); ++i) {
497 +      if ( (*i) == unique_id_2 ) return true;
498 +    }    
499 + #else
500 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
501 +         i != skipsForLocalAtom[atom1].end(); ++i) {
502 +      if ( (*i) == unique_id_2 ) return true;
503 +    }    
504 + #endif
505    }
506  
507 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
508 +    
509 + #ifdef IS_MPI
510 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
511 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
512 +    }
513 + #else
514 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
515 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
516 +    }
517 + #endif
518 +
519 +    // zero is default for unconnected (i.e. normal) pair interactions
520 +    return 0;
521 +  }
522 +
523    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
524   #ifdef IS_MPI
525      atomRowData.force[atom1] += fg;
# Line 320 | Line 541 | namespace OpenMD {
541      InteractionData idat;
542  
543   #ifdef IS_MPI
544 +    
545 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
546 +                             ff_->getAtomType(identsCol[atom2]) );
547 +
548      if (storageLayout_ & DataStorage::dslAmat) {
549        idat.A1 = &(atomRowData.aMat[atom1]);
550        idat.A2 = &(atomColData.aMat[atom2]);
# Line 344 | Line 569 | namespace OpenMD {
569        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
570        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
571      }
572 +
573   #else
574 +
575 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
576 +                             ff_->getAtomType(identsLocal[atom2]) );
577 +
578      if (storageLayout_ & DataStorage::dslAmat) {
579        idat.A1 = &(snap_->atomData.aMat[atom1]);
580        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 377 | Line 607 | namespace OpenMD {
607  
608      InteractionData idat;
609   #ifdef IS_MPI
610 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
611 +                             ff_->getAtomType(identsCol[atom2]) );
612 +
613      if (storageLayout_ & DataStorage::dslElectroFrame) {
614        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
615        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 390 | Line 623 | namespace OpenMD {
623        idat.t2 = &(atomColData.force[atom2]);
624      }
625   #else
626 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
627 +                             ff_->getAtomType(identsLocal[atom2]) );
628 +
629      if (storageLayout_ & DataStorage::dslElectroFrame) {
630        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
631        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
# Line 402 | Line 638 | namespace OpenMD {
638        idat.t1 = &(snap_->atomData.force[atom1]);
639        idat.t2 = &(snap_->atomData.force[atom2]);
640      }
641 < #endif
406 <    
641 > #endif    
642    }
643  
409 –
410 –
411 –
644    /*
645     * buildNeighborList
646     *

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