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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 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
Revision 1584 by gezelter, Fri Jun 17 20:16:35 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 < #ifdef IS_MPI    
59 <    int nLocal = snap_->getNumberOfAtoms();
59 <    int nGroups = snap_->getNumberOfCutoffGroups();
60 <    
61 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
62 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
58 >    ff_ = info_->getForceField();
59 >    nLocal_ = snap_->getNumberOfAtoms();
60  
61 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
62 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
63 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
64 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63 >    // gather the information for atomtype IDs (atids):
64 >    idents = info_->getIdentArray();
65 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
66 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
67 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 >    massFactors = info_->getMassFactors();
69  
70 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
71 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
72 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
73 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
70 >    PairList excludes = info_->getExcludedInteractions();
71 >    PairList oneTwo = info_->getOneTwoInteractions();
72 >    PairList oneThree = info_->getOneThreeInteractions();
73 >    PairList oneFour = info_->getOneFourInteractions();
74  
75 <    int nAtomsInRow = AtomCommIntRow->getSize();
76 <    int nAtomsInCol = AtomCommIntColumn->getSize();
77 <    int nGroupsInRow = cgCommIntRow->getSize();
78 <    int nGroupsInCol = cgCommIntColumn->getSize();
75 > #ifdef IS_MPI
76 >
77 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
78 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 >    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
82  
83 +    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
84 +    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
85 +    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
86 +    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
87 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
88 +
89 +    cgCommIntRow = new Communicator<Row,int>(nGroups_);
90 +    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
91 +    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
92 +    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
93 +
94 +    nAtomsInRow_ = AtomCommIntRow->getSize();
95 +    nAtomsInCol_ = AtomCommIntColumn->getSize();
96 +    nGroupsInRow_ = cgCommIntRow->getSize();
97 +    nGroupsInCol_ = cgCommIntColumn->getSize();
98 +
99      // Modify the data storage objects with the correct layouts and sizes:
100 <    atomRowData.resize(nAtomsInRow);
100 >    atomRowData.resize(nAtomsInRow_);
101      atomRowData.setStorageLayout(storageLayout_);
102 <    atomColData.resize(nAtomsInCol);
102 >    atomColData.resize(nAtomsInCol_);
103      atomColData.setStorageLayout(storageLayout_);
104 <    cgRowData.resize(nGroupsInRow);
104 >    cgRowData.resize(nGroupsInRow_);
105      cgRowData.setStorageLayout(DataStorage::dslPosition);
106 <    cgColData.resize(nGroupsInCol);
106 >    cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108 +        
109 +    identsRow.resize(nAtomsInRow_);
110 +    identsCol.resize(nAtomsInCol_);
111      
112 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
113 <                                      vector<RealType> (nAtomsInRow, 0.0));
93 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94 <                                      vector<RealType> (nAtomsInCol, 0.0));
95 <
96 <
97 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
99 –    // gather the information for atomtype IDs (atids):
100 –    vector<int> identsLocal = info_->getIdentArray();
101 –    identsRow.reserve(nAtomsInRow);
102 –    identsCol.reserve(nAtomsInCol);
103 –    
104 –    AtomCommIntRow->gather(identsLocal, identsRow);
105 –    AtomCommIntColumn->gather(identsLocal, identsCol);
106 –    
107 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117      
111 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    // still need:
122 <    // topoDist
123 <    // exclude
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123 >
124 >    groupListRow_.clear();
125 >    groupListRow_.resize(nGroupsInRow_);
126 >    for (int i = 0; i < nGroupsInRow_; i++) {
127 >      int gid = cgRowToGlobal[i];
128 >      for (int j = 0; j < nAtomsInRow_; j++) {
129 >        int aid = AtomRowToGlobal[j];
130 >        if (globalGroupMembership[aid] == gid)
131 >          groupListRow_[i].push_back(j);
132 >      }      
133 >    }
134 >
135 >    groupListCol_.clear();
136 >    groupListCol_.resize(nGroupsInCol_);
137 >    for (int i = 0; i < nGroupsInCol_; i++) {
138 >      int gid = cgColToGlobal[i];
139 >      for (int j = 0; j < nAtomsInCol_; j++) {
140 >        int aid = AtomColToGlobal[j];
141 >        if (globalGroupMembership[aid] == gid)
142 >          groupListCol_[i].push_back(j);
143 >      }      
144 >    }
145 >
146 >    skipsForAtom.clear();
147 >    skipsForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152 >    for (int i = 0; i < nAtomsInRow_; i++) {
153 >      int iglob = AtomRowToGlobal[i];
154 >
155 >      for (int j = 0; j < nAtomsInCol_; j++) {
156 >        int jglob = AtomColToGlobal[j];
157 >
158 >        if (excludes.hasPair(iglob, jglob))
159 >          skipsForAtom[i].push_back(j);      
160 >        
161 >        if (oneTwo.hasPair(iglob, jglob)) {
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree.hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour.hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174 >        }
175 >      }      
176 >    }
177 >
178 > #endif
179 >
180 >    groupList_.clear();
181 >    groupList_.resize(nGroups_);
182 >    for (int i = 0; i < nGroups_; i++) {
183 >      int gid = cgLocalToGlobal[i];
184 >      for (int j = 0; j < nLocal_; j++) {
185 >        int aid = AtomLocalToGlobal[j];
186 >        if (globalGroupMembership[aid] == gid) {
187 >          groupList_[i].push_back(j);
188 >        }
189 >      }      
190 >    }
191 >
192 >    skipsForAtom.clear();
193 >    skipsForAtom.resize(nLocal_);
194 >    toposForAtom.clear();
195 >    toposForAtom.resize(nLocal_);
196 >    topoDist.clear();
197 >    topoDist.resize(nLocal_);
198 >
199 >    for (int i = 0; i < nLocal_; i++) {
200 >      int iglob = AtomLocalToGlobal[i];
201 >
202 >      for (int j = 0; j < nLocal_; j++) {
203 >        int jglob = AtomLocalToGlobal[j];
204 >
205 >        if (excludes.hasPair(iglob, jglob))
206 >          skipsForAtom[i].push_back(j);              
207 >        
208 >        if (oneTwo.hasPair(iglob, jglob)) {
209 >          toposForAtom[i].push_back(j);
210 >          topoDist[i].push_back(1);
211 >        } else {
212 >          if (oneThree.hasPair(iglob, jglob)) {
213 >            toposForAtom[i].push_back(j);
214 >            topoDist[i].push_back(2);
215 >          } else {
216 >            if (oneFour.hasPair(iglob, jglob)) {
217 >              toposForAtom[i].push_back(j);
218 >              topoDist[i].push_back(3);
219 >            }
220 >          }
221 >        }
222 >      }      
223 >    }
224 >    
225 >    createGtypeCutoffMap();
226 >  }
227 >  
228 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
229 >
230 >    RealType tol = 1e-6;
231 >    RealType rc;
232 >    int atid;
233 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234 >    vector<RealType> atypeCutoff;
235 >    atypeCutoff.resize( atypes.size() );
236 >      
237 >    for (set<AtomType*>::iterator at = atypes.begin();
238 >         at != atypes.end(); ++at){
239 >      atid = (*at)->getIdent();
240 >
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245 >    }
246 >
247 >    vector<RealType> gTypeCutoffs;
248 >
249 >    // first we do a single loop over the cutoff groups to find the
250 >    // largest cutoff for any atypes present in this group.
251 > #ifdef IS_MPI
252 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 >    groupRowToGtype.resize(nGroupsInRow_);
254 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
256 >      for (vector<int>::iterator ia = atomListRow.begin();
257 >           ia != atomListRow.end(); ++ia) {            
258 >        int atom1 = (*ia);
259 >        atid = identsRow[atom1];
260 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261 >          groupCutoffRow[cg1] = atypeCutoff[atid];
262 >        }
263 >      }
264 >
265 >      bool gTypeFound = false;
266 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
267 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
268 >          groupRowToGtype[cg1] = gt;
269 >          gTypeFound = true;
270 >        }
271 >      }
272 >      if (!gTypeFound) {
273 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
274 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
275 >      }
276 >      
277 >    }
278 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279 >    groupColToGtype.resize(nGroupsInCol_);
280 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282 >      for (vector<int>::iterator jb = atomListCol.begin();
283 >           jb != atomListCol.end(); ++jb) {            
284 >        int atom2 = (*jb);
285 >        atid = identsCol[atom2];
286 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287 >          groupCutoffCol[cg2] = atypeCutoff[atid];
288 >        }
289 >      }
290 >      bool gTypeFound = false;
291 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293 >          groupColToGtype[cg2] = gt;
294 >          gTypeFound = true;
295 >        }
296 >      }
297 >      if (!gTypeFound) {
298 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300 >      }
301 >    }
302 > #else
303 >
304 >    vector<RealType> groupCutoff(nGroups_, 0.0);
305 >    groupToGtype.resize(nGroups_);
306 >
307 >    cerr << "nGroups = " << nGroups_ << "\n";
308 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 >
310 >      groupCutoff[cg1] = 0.0;
311 >      vector<int> atomList = getAtomsInGroupRow(cg1);
312 >
313 >      for (vector<int>::iterator ia = atomList.begin();
314 >           ia != atomList.end(); ++ia) {            
315 >        int atom1 = (*ia);
316 >        atid = idents[atom1];
317 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
318 >          groupCutoff[cg1] = atypeCutoff[atid];
319 >        }
320 >      }
321 >
322 >      bool gTypeFound = false;
323 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325 >          groupToGtype[cg1] = gt;
326 >          gTypeFound = true;
327 >        }
328 >      }
329 >      if (!gTypeFound) {
330 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
331 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332 >      }      
333 >    }
334   #endif
335 +
336 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
337 +    // Now we find the maximum group cutoff value present in the simulation
338 +
339 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
340 +
341 + #ifdef IS_MPI
342 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
343 + #endif
344 +    
345 +    RealType tradRcut = groupMax;
346 +
347 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
348 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
349 +        RealType thisRcut;
350 +        switch(cutoffPolicy_) {
351 +        case TRADITIONAL:
352 +          thisRcut = tradRcut;
353 +          break;
354 +        case MIX:
355 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
356 +          break;
357 +        case MAX:
358 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
359 +          break;
360 +        default:
361 +          sprintf(painCave.errMsg,
362 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
363 +                  "hit an unknown cutoff policy!\n");
364 +          painCave.severity = OPENMD_ERROR;
365 +          painCave.isFatal = 1;
366 +          simError();
367 +          break;
368 +        }
369 +
370 +        pair<int,int> key = make_pair(i,j);
371 +        gTypeCutoffMap[key].first = thisRcut;
372 +
373 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
374 +
375 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
376 +        
377 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
378 +
379 +        // sanity check
380 +        
381 +        if (userChoseCutoff_) {
382 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
383 +            sprintf(painCave.errMsg,
384 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
385 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
386 +            painCave.severity = OPENMD_ERROR;
387 +            painCave.isFatal = 1;
388 +            simError();            
389 +          }
390 +        }
391 +      }
392 +    }
393    }
394 +
395 +
396 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
397 +    int i, j;  
398 + #ifdef IS_MPI
399 +    i = groupRowToGtype[cg1];
400 +    j = groupColToGtype[cg2];
401 + #else
402 +    i = groupToGtype[cg1];
403 +    j = groupToGtype[cg2];
404 + #endif    
405 +    return gTypeCutoffMap[make_pair(i,j)];
406 +  }
407 +
408 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
409 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
410 +      if (toposForAtom[atom1][j] == atom2)
411 +        return topoDist[atom1][j];
412 +    }
413 +    return 0;
414 +  }
415 +
416 +  void ForceMatrixDecomposition::zeroWorkArrays() {
417 +    pairwisePot = 0.0;
418 +    embeddingPot = 0.0;
419 +
420 + #ifdef IS_MPI
421 +    if (storageLayout_ & DataStorage::dslForce) {
422 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
423 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
424 +    }
425 +
426 +    if (storageLayout_ & DataStorage::dslTorque) {
427 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
428 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
429 +    }
430      
431 +    fill(pot_row.begin(), pot_row.end(),
432 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
433  
434 +    fill(pot_col.begin(), pot_col.end(),
435 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
436  
437 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
438 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
439 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
440 +    }
441 +
442 +    if (storageLayout_ & DataStorage::dslDensity) {      
443 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
444 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
445 +    }
446 +
447 +    if (storageLayout_ & DataStorage::dslFunctional) {  
448 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
449 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
450 +    }
451 +
452 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
453 +      fill(atomRowData.functionalDerivative.begin(),
454 +           atomRowData.functionalDerivative.end(), 0.0);
455 +      fill(atomColData.functionalDerivative.begin(),
456 +           atomColData.functionalDerivative.end(), 0.0);
457 +    }
458 +
459 + #else
460 +    
461 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
462 +      fill(snap_->atomData.particlePot.begin(),
463 +           snap_->atomData.particlePot.end(), 0.0);
464 +    }
465 +    
466 +    if (storageLayout_ & DataStorage::dslDensity) {      
467 +      fill(snap_->atomData.density.begin(),
468 +           snap_->atomData.density.end(), 0.0);
469 +    }
470 +    if (storageLayout_ & DataStorage::dslFunctional) {
471 +      fill(snap_->atomData.functional.begin(),
472 +           snap_->atomData.functional.end(), 0.0);
473 +    }
474 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
475 +      fill(snap_->atomData.functionalDerivative.begin(),
476 +           snap_->atomData.functionalDerivative.end(), 0.0);
477 +    }
478 + #endif
479 +    
480 +  }
481 +
482 +
483    void ForceMatrixDecomposition::distributeData()  {
484      snap_ = sman_->getCurrentSnapshot();
485      storageLayout_ = sman_->getStorageLayout();
# Line 155 | Line 515 | namespace OpenMD {
515   #endif      
516    }
517    
518 +  /* collects information obtained during the pre-pair loop onto local
519 +   * data structures.
520 +   */
521    void ForceMatrixDecomposition::collectIntermediateData() {
522      snap_ = sman_->getCurrentSnapshot();
523      storageLayout_ = sman_->getStorageLayout();
# Line 166 | Line 529 | namespace OpenMD {
529                                 snap_->atomData.density);
530        
531        int n = snap_->atomData.density.size();
532 <      std::vector<RealType> rho_tmp(n, 0.0);
532 >      vector<RealType> rho_tmp(n, 0.0);
533        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
534        for (int i = 0; i < n; i++)
535          snap_->atomData.density[i] += rho_tmp[i];
536      }
537   #endif
538    }
539 <  
539 >
540 >  /*
541 >   * redistributes information obtained during the pre-pair loop out to
542 >   * row and column-indexed data structures
543 >   */
544    void ForceMatrixDecomposition::distributeIntermediateData() {
545      snap_ = sman_->getCurrentSnapshot();
546      storageLayout_ = sman_->getStorageLayout();
# Line 229 | Line 596 | namespace OpenMD {
596          snap_->atomData.torque[i] += trq_tmp[i];
597      }
598      
599 <    int nLocal = snap_->getNumberOfAtoms();
599 >    nLocal_ = snap_->getNumberOfAtoms();
600  
601 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
602 <                                       vector<RealType> (nLocal, 0.0));
603 <    
604 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
605 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
606 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
607 <        pot_local[i] += pot_temp[i][ii];
608 <      }
609 <    }
601 >    vector<potVec> pot_temp(nLocal_,
602 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
603 >
604 >    // scatter/gather pot_row into the members of my column
605 >          
606 >    AtomCommPotRow->scatter(pot_row, pot_temp);
607 >
608 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
609 >      pairwisePot += pot_temp[ii];
610 >    
611 >    fill(pot_temp.begin(), pot_temp.end(),
612 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
613 >      
614 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
615 >    
616 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
617 >      pairwisePot += pot_temp[ii];    
618   #endif
619 +
620    }
621  
622 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
623 + #ifdef IS_MPI
624 +    return nAtomsInRow_;
625 + #else
626 +    return nLocal_;
627 + #endif
628 +  }
629 +
630 +  /**
631 +   * returns the list of atoms belonging to this group.  
632 +   */
633 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
634 + #ifdef IS_MPI
635 +    return groupListRow_[cg1];
636 + #else
637 +    return groupList_[cg1];
638 + #endif
639 +  }
640 +
641 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
642 + #ifdef IS_MPI
643 +    return groupListCol_[cg2];
644 + #else
645 +    return groupList_[cg2];
646 + #endif
647 +  }
648    
649    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
650      Vector3d d;
# Line 284 | Line 686 | namespace OpenMD {
686      snap_->wrapVector(d);
687      return d;    
688    }
689 +
690 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
691 + #ifdef IS_MPI
692 +    return massFactorsRow[atom1];
693 + #else
694 +    cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
695 +    return massFactors[atom1];
696 + #endif
697 +  }
698 +
699 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
700 + #ifdef IS_MPI
701 +    return massFactorsCol[atom2];
702 + #else
703 +    return massFactors[atom2];
704 + #endif
705 +
706 +  }
707      
708    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
709      Vector3d d;
# Line 298 | Line 718 | namespace OpenMD {
718      return d;    
719    }
720  
721 +  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
722 +    return skipsForAtom[atom1];
723 +  }
724 +
725 +  /**
726 +   * There are a number of reasons to skip a pair or a
727 +   * particle. Mostly we do this to exclude atoms who are involved in
728 +   * short range interactions (bonds, bends, torsions), but we also
729 +   * need to exclude some overcounted interactions that result from
730 +   * the parallel decomposition.
731 +   */
732 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
733 +    int unique_id_1, unique_id_2;
734 +
735 + #ifdef IS_MPI
736 +    // in MPI, we have to look up the unique IDs for each atom
737 +    unique_id_1 = AtomRowToGlobal[atom1];
738 +    unique_id_2 = AtomColToGlobal[atom2];
739 +
740 +    // this situation should only arise in MPI simulations
741 +    if (unique_id_1 == unique_id_2) return true;
742 +    
743 +    // this prevents us from doing the pair on multiple processors
744 +    if (unique_id_1 < unique_id_2) {
745 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
746 +    } else {
747 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
748 +    }
749 + #else
750 +    // in the normal loop, the atom numbers are unique
751 +    unique_id_1 = atom1;
752 +    unique_id_2 = atom2;
753 + #endif
754 +    
755 +    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
756 +         i != skipsForAtom[atom1].end(); ++i) {
757 +      if ( (*i) == unique_id_2 ) return true;
758 +    }
759 +
760 +    return false;
761 +  }
762 +
763 +
764    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
765   #ifdef IS_MPI
766      atomRowData.force[atom1] += fg;
# Line 312 | Line 775 | namespace OpenMD {
775   #else
776      snap_->atomData.force[atom2] += fg;
777   #endif
315 –
778    }
779  
780      // filling interaction blocks with pointers
781 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
782 <
321 <    InteractionData idat;
781 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
782 >                                                     int atom1, int atom2) {    
783   #ifdef IS_MPI
784 +    
785 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786 +                             ff_->getAtomType(identsCol[atom2]) );
787 +    
788      if (storageLayout_ & DataStorage::dslAmat) {
789        idat.A1 = &(atomRowData.aMat[atom1]);
790        idat.A2 = &(atomColData.aMat[atom2]);
791      }
792 <
792 >    
793      if (storageLayout_ & DataStorage::dslElectroFrame) {
794        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
795        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 340 | Line 805 | namespace OpenMD {
805        idat.rho2 = &(atomColData.density[atom2]);
806      }
807  
808 +    if (storageLayout_ & DataStorage::dslFunctional) {
809 +      idat.frho1 = &(atomRowData.functional[atom1]);
810 +      idat.frho2 = &(atomColData.functional[atom2]);
811 +    }
812 +
813      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
814        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
815        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
816      }
817 +
818 +    if (storageLayout_ & DataStorage::dslParticlePot) {
819 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
820 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
821 +    }
822 +
823   #else
824 +
825 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
826 +                             ff_->getAtomType(idents[atom2]) );
827 +
828      if (storageLayout_ & DataStorage::dslAmat) {
829        idat.A1 = &(snap_->atomData.aMat[atom1]);
830        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 840 | namespace OpenMD {
840        idat.t2 = &(snap_->atomData.torque[atom2]);
841      }
842  
843 <    if (storageLayout_ & DataStorage::dslDensity) {
843 >    if (storageLayout_ & DataStorage::dslDensity) {    
844        idat.rho1 = &(snap_->atomData.density[atom1]);
845        idat.rho2 = &(snap_->atomData.density[atom2]);
846      }
847  
848 +    if (storageLayout_ & DataStorage::dslFunctional) {
849 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
850 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
851 +    }
852 +
853      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
854        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
855        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
856      }
857 +
858 +    if (storageLayout_ & DataStorage::dslParticlePot) {
859 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
860 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
861 +    }
862 +
863   #endif
373 –    
864    }
865 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
866 <    InteractionData idat;
867 <    skippedCharge1
378 <      skippedCharge2
379 <      rij
380 <      d
381 <    electroMult
382 <    sw
383 <    f
865 >
866 >  
867 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
868   #ifdef IS_MPI
869 +    pot_row[atom1] += 0.5 *  *(idat.pot);
870 +    pot_col[atom2] += 0.5 *  *(idat.pot);
871  
872 +    atomRowData.force[atom1] += *(idat.f1);
873 +    atomColData.force[atom2] -= *(idat.f1);
874 + #else
875 +    pairwisePot += *(idat.pot);
876 +
877 +    snap_->atomData.force[atom1] += *(idat.f1);
878 +    snap_->atomData.force[atom2] -= *(idat.f1);
879 + #endif
880 +
881 +  }
882 +
883 +
884 +  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885 +                                              int atom1, int atom2) {
886 + #ifdef IS_MPI
887 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888 +                             ff_->getAtomType(identsCol[atom2]) );
889 +
890      if (storageLayout_ & DataStorage::dslElectroFrame) {
891        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893      }
894 +
895      if (storageLayout_ & DataStorage::dslTorque) {
896        idat.t1 = &(atomRowData.torque[atom1]);
897        idat.t2 = &(atomColData.torque[atom2]);
898      }
899  
900 <    
900 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
901 >      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902 >      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903 >    }
904 > #else
905 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906 >                             ff_->getAtomType(idents[atom2]) );
907 >
908 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
909 >      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910 >      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911 >    }
912 >
913 >    if (storageLayout_ & DataStorage::dslTorque) {
914 >      idat.t1 = &(snap_->atomData.torque[atom1]);
915 >      idat.t2 = &(snap_->atomData.torque[atom2]);
916 >    }
917 >
918 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
919 >      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920 >      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921 >    }
922 > #endif    
923    }
924 <  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
924 >
925 >
926 >  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
927 > #ifdef IS_MPI
928 >    pot_row[atom1] += 0.5 *  *(idat.pot);
929 >    pot_col[atom2] += 0.5 *  *(idat.pot);
930 > #else
931 >    pairwisePot += *(idat.pot);  
932 > #endif
933 >
934    }
935  
936  
# Line 404 | Line 940 | namespace OpenMD {
940     * first element of pair is row-indexed CutoffGroup
941     * second element of pair is column-indexed CutoffGroup
942     */
943 <  vector<pair<int, int> >  buildNeighborList() {
944 <    Vector3d dr, invWid, rs, shift;
945 <    Vector3i cc, m1v, m2s;
946 <    RealType rrNebr;
947 <    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
943 >  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
944 >      
945 >    vector<pair<int, int> > neighborList;
946 >    groupCutoffs cuts;
947 > #ifdef IS_MPI
948 >    cellListRow_.clear();
949 >    cellListCol_.clear();
950 > #else
951 >    cellList_.clear();
952 > #endif
953  
954 <
955 <    vector<pair<int, int> > neighborList;  
956 <    Vector3i nCells;
416 <    Vector3d invWid, r;
417 <
418 <    rList_ = (rCut_ + skinThickness_);
419 <    rl2 = rList_ * rList_;
420 <
421 <    snap_ = sman_->getCurrentSnapshot();
954 >    RealType rList_ = (largestRcut_ + skinThickness_);
955 >    RealType rl2 = rList_ * rList_;
956 >    Snapshot* snap_ = sman_->getCurrentSnapshot();
957      Mat3x3d Hmat = snap_->getHmat();
958      Vector3d Hx = Hmat.getColumn(0);
959      Vector3d Hy = Hmat.getColumn(1);
960      Vector3d Hz = Hmat.getColumn(2);
961  
962 <    nCells.x() = (int) ( Hx.length() )/ rList_;
963 <    nCells.y() = (int) ( Hy.length() )/ rList_;
964 <    nCells.z() = (int) ( Hz.length() )/ rList_;
962 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
963 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
964 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
965  
966 <    for (i = 0; i < nGroupsInRow; i++) {
966 >    Mat3x3d invHmat = snap_->getInvHmat();
967 >    Vector3d rs, scaled, dr;
968 >    Vector3i whichCell;
969 >    int cellIndex;
970 >    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
971 >
972 > #ifdef IS_MPI
973 >    cellListRow_.resize(nCtot);
974 >    cellListCol_.resize(nCtot);
975 > #else
976 >    cellList_.resize(nCtot);
977 > #endif
978 >
979 > #ifdef IS_MPI
980 >    for (int i = 0; i < nGroupsInRow_; i++) {
981        rs = cgRowData.position[i];
982 <      snap_->scaleVector(rs);    
982 >
983 >      // scaled positions relative to the box vectors
984 >      scaled = invHmat * rs;
985 >
986 >      // wrap the vector back into the unit box by subtracting integer box
987 >      // numbers
988 >      for (int j = 0; j < 3; j++) {
989 >        scaled[j] -= roundMe(scaled[j]);
990 >        scaled[j] += 0.5;
991 >      }
992 >    
993 >      // find xyz-indices of cell that cutoffGroup is in.
994 >      whichCell.x() = nCells_.x() * scaled.x();
995 >      whichCell.y() = nCells_.y() * scaled.y();
996 >      whichCell.z() = nCells_.z() * scaled.z();
997 >
998 >      // find single index of this cell:
999 >      cellIndex = Vlinear(whichCell, nCells_);
1000 >
1001 >      // add this cutoff group to the list of groups in this cell;
1002 >      cellListRow_[cellIndex].push_back(i);
1003      }
435 –    
1004  
1005 <    VDiv (invWid, cells, region);
1006 <    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
1007 <    for (n = 0; n < nMol; n ++) {
1008 <      VSAdd (rs, mol[n].r, 0.5, region);
1009 <      VMul (cc, rs, invWid);
1010 <      c = VLinear (cc, cells) + nMol;
1011 <      cellList[n] = cellList[c];
1012 <      cellList[c] = n;
1005 >    for (int i = 0; i < nGroupsInCol_; i++) {
1006 >      rs = cgColData.position[i];
1007 >
1008 >      // scaled positions relative to the box vectors
1009 >      scaled = invHmat * rs;
1010 >
1011 >      // wrap the vector back into the unit box by subtracting integer box
1012 >      // numbers
1013 >      for (int j = 0; j < 3; j++) {
1014 >        scaled[j] -= roundMe(scaled[j]);
1015 >        scaled[j] += 0.5;
1016 >      }
1017 >
1018 >      // find xyz-indices of cell that cutoffGroup is in.
1019 >      whichCell.x() = nCells_.x() * scaled.x();
1020 >      whichCell.y() = nCells_.y() * scaled.y();
1021 >      whichCell.z() = nCells_.z() * scaled.z();
1022 >
1023 >      // find single index of this cell:
1024 >      cellIndex = Vlinear(whichCell, nCells_);
1025 >
1026 >      // add this cutoff group to the list of groups in this cell;
1027 >      cellListCol_[cellIndex].push_back(i);
1028      }
1029 <    nebrTabLen = 0;
1030 <    for (m1z = 0; m1z < cells.z(); m1z++) {
1031 <      for (m1y = 0; m1y < cells.y(); m1y++) {
1032 <        for (m1x = 0; m1x < cells.x(); m1x++) {
1029 > #else
1030 >    for (int i = 0; i < nGroups_; i++) {
1031 >      rs = snap_->cgData.position[i];
1032 >
1033 >      // scaled positions relative to the box vectors
1034 >      scaled = invHmat * rs;
1035 >
1036 >      // wrap the vector back into the unit box by subtracting integer box
1037 >      // numbers
1038 >      for (int j = 0; j < 3; j++) {
1039 >        scaled[j] -= roundMe(scaled[j]);
1040 >        scaled[j] += 0.5;
1041 >      }
1042 >
1043 >      // find xyz-indices of cell that cutoffGroup is in.
1044 >      whichCell.x() = nCells_.x() * scaled.x();
1045 >      whichCell.y() = nCells_.y() * scaled.y();
1046 >      whichCell.z() = nCells_.z() * scaled.z();
1047 >
1048 >      // find single index of this cell:
1049 >      cellIndex = Vlinear(whichCell, nCells_);      
1050 >
1051 >      // add this cutoff group to the list of groups in this cell;
1052 >      cellList_[cellIndex].push_back(i);
1053 >    }
1054 > #endif
1055 >
1056 >    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1057 >      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1058 >        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1059            Vector3i m1v(m1x, m1y, m1z);
1060 <          m1 = VLinear(m1v, cells) + nMol;
452 <          for (offset = 0; offset < nOffset_; offset++) {
453 <            m2v = m1v + cellOffsets_[offset];
454 <            shift = V3Zero();
1060 >          int m1 = Vlinear(m1v, nCells_);
1061  
1062 <            if (m2v.x() >= cells.x) {
1062 >          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1063 >               os != cellOffsets_.end(); ++os) {
1064 >            
1065 >            Vector3i m2v = m1v + (*os);
1066 >            
1067 >            if (m2v.x() >= nCells_.x()) {
1068                m2v.x() = 0;          
458 –              shift.x() = region.x();  
1069              } else if (m2v.x() < 0) {
1070 <              m2v.x() = cells.x() - 1;
461 <              shift.x() = - region.x();
1070 >              m2v.x() = nCells_.x() - 1;
1071              }
1072 <
1073 <            if (m2v.y() >= cells.y()) {
1072 >            
1073 >            if (m2v.y() >= nCells_.y()) {
1074                m2v.y() = 0;          
466 –              shift.y() = region.y();  
1075              } else if (m2v.y() < 0) {
1076 <              m2v.y() = cells.y() - 1;
469 <              shift.y() = - region.y();
1076 >              m2v.y() = nCells_.y() - 1;
1077              }
1078 +            
1079 +            if (m2v.z() >= nCells_.z()) {
1080 +              m2v.z() = 0;          
1081 +            } else if (m2v.z() < 0) {
1082 +              m2v.z() = nCells_.z() - 1;
1083 +            }
1084 +            
1085 +            int m2 = Vlinear (m2v, nCells_);
1086  
1087 <            m2 = VLinear (m2v, cells) + nMol;
1088 <            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
1089 <              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
1090 <                if (m1 != m2 || j2 < j1) {
1091 <                  dr = mol[j1].r - mol[j2].r;
1092 <                  VSub (dr, mol[j1].r, mol[j2].r);
1093 <                  VVSub (dr, shift);
1094 <                  if (VLenSq (dr) < rrNebr) {
1095 <                    neighborList.push_back(make_pair(j1, j2));
1087 > #ifdef IS_MPI
1088 >            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1089 >                 j1 != cellListRow_[m1].end(); ++j1) {
1090 >              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1091 >                   j2 != cellListCol_[m2].end(); ++j2) {
1092 >                              
1093 >                // Always do this if we're in different cells or if
1094 >                // we're in the same cell and the global index of the
1095 >                // j2 cutoff group is less than the j1 cutoff group
1096 >
1097 >                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1098 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1099 >                  snap_->wrapVector(dr);
1100 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1101 >                  if (dr.lengthSquare() < cuts.third) {
1102 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1103                    }
1104                  }
1105                }
1106              }
1107 + #else
1108 +
1109 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
1110 +                 j1 != cellList_[m1].end(); ++j1) {
1111 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
1112 +                   j2 != cellList_[m2].end(); ++j2) {
1113 +
1114 +                // Always do this if we're in different cells or if
1115 +                // we're in the same cell and the global index of the
1116 +                // j2 cutoff group is less than the j1 cutoff group
1117 +
1118 +                if (m2 != m1 || (*j2) < (*j1)) {
1119 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1120 +                  snap_->wrapVector(dr);
1121 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1122 +                  if (dr.lengthSquare() < cuts.third) {
1123 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1124 +                  }
1125 +                }
1126 +              }
1127 +            }
1128 + #endif
1129            }
1130          }
1131        }
1132      }
1133 +    
1134 +    // save the local cutoff group positions for the check that is
1135 +    // done on each loop:
1136 +    saved_CG_positions_.clear();
1137 +    for (int i = 0; i < nGroups_; i++)
1138 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1139 +  
1140 +    return neighborList;
1141    }
490 –
491 –  
1142   } //end namespace OpenMD

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