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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1538 by chuckv, Tue Jan 11 18:58:12 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC

# Line 1 | Line 1
1 < /**
2 < * @file ForceDecomposition.cpp
3 < * @author Charles Vardeman <cvardema.at.nd.edu>
4 < * @date 08/18/2010
5 < * @time 11:56am
6 < * @version 1.0
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
8 – * @section LICENSE
9 – * Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
10 – *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
6   * redistribute this software in source and binary code form, provided
# Line 45 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 + #include "parallel/ForceMatrixDecomposition.hpp"
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 {
49  
50 +  /**
51 +   * distributeInitialData is essentially a copy of the older fortran
52 +   * SimulationSetup
53 +   */
54 +  
55 +  void ForceMatrixDecomposition::distributeInitialData() {
56 +    snap_ = sman_->getCurrentSnapshot();
57 +    storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59 +    nLocal_ = snap_->getNumberOfAtoms();
60  
61 < /*  -*- c++ -*-  */
62 < #include "config.h"
63 < #include <stdlib.h>
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 >    PairList excludes = info_->getExcludedInteractions();
71 >    PairList oneTwo = info_->getOneTwoInteractions();
72 >    PairList oneThree = info_->getOneThreeInteractions();
73 >    PairList oneFour = info_->getOneFourInteractions();
74 >
75   #ifdef IS_MPI
76 < #include <mpi.h>
77 < #endif
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 < #include <iostream>
84 < #include <vector>
85 < #include <algorithm>
86 < #include <cmath>
87 < #include "parallel/ForceDecomposition.hpp"
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 < using namespace std;
95 < using namespace OpenMD;
94 >    nAtomsInRow_ = AtomCommIntRow->getSize();
95 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
96 >    nGroupsInRow_ = cgCommIntRow->getSize();
97 >    nGroupsInCol_ = cgCommIntColumn->getSize();
98  
99 < //__static
100 < #ifdef IS_MPI
101 < static vector<MPI:Comm> communictors;
102 < #endif
99 >    // Modify the data storage objects with the correct layouts and sizes:
100 >    atomRowData.resize(nAtomsInRow_);
101 >    atomRowData.setStorageLayout(storageLayout_);
102 >    atomColData.resize(nAtomsInCol_);
103 >    atomColData.setStorageLayout(storageLayout_);
104 >    cgRowData.resize(nGroupsInRow_);
105 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
106 >    cgColData.resize(nGroupsInCol_);
107 >    cgColData.setStorageLayout(DataStorage::dslPosition);
108 >        
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111 >    
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114 >    
115 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117 >    
118 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 < //____ MPITypeTraits
122 < template<typename T>
75 < struct MPITypeTraits;
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124 < #ifdef IS_MPI
125 < template<>
126 < struct MPITypeTraits<RealType> {
127 <  static const MPI::Datatype datatype;
128 < };
129 < const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
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 < template<>
136 < struct MPITypeTraits<int> {
137 <  static const MPI::Datatype datatype;
138 < };
139 < const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
140 < #endif
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 < /**
147 < * Constructor for ForceDecomposition Parallel Decomposition Method
148 < * Will try to construct a symmetric grid of processors. Ideally, the
149 < * number of processors will be a square ex: 4, 9, 16, 25.
150 < *
151 < */
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 < ForceDecomposition::ForceDecomposition() {
155 >      for (int j = 0; j < nAtomsInCol_; j++) {
156 >        int jglob = AtomColToGlobal[j];
157  
158 < #ifdef IS_MPI
159 <  int nProcs = MPI::COMM_WORLD.Get_size();
160 <  int worldRank = MPI::COMM_WORLD.Get_rank();
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 <  // First time through, construct column stride.
181 <  if (communicators.size() == 0)
182 <  {
183 <    int nColumnsMax = (int) round(sqrt((float) nProcs));
184 <    for (int i = 0; i < nProcs; ++i)
185 <    {
186 <      if (nProcs%i==0) nColumns=i;
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 <    int nRows = nProcs/nColumns;    
193 <    myRank_ = (int) worldRank%nColumns;
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 <  else
228 <  {
119 <    myRank_ = myRank/nColumns;
120 <  }
121 <  MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
122 <  
123 <  isColumn_ = false;
124 <  
125 < }
227 >  
228 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
229  
230 < ForceDecomposition::gather(sendbuf, receivebuf){
231 <  communicators(myIndex_).Allgatherv();
232 < }
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 < ForceDecomposition::scatter(sbuffer, rbuffer){
250 <  communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
251 < }
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();
486 + #ifdef IS_MPI
487 +    
488 +    // gather up the atomic positions
489 +    AtomCommVectorRow->gather(snap_->atomData.position,
490 +                              atomRowData.position);
491 +    AtomCommVectorColumn->gather(snap_->atomData.position,
492 +                                 atomColData.position);
493 +    
494 +    // gather up the cutoff group positions
495 +    cgCommVectorRow->gather(snap_->cgData.position,
496 +                            cgRowData.position);
497 +    cgCommVectorColumn->gather(snap_->cgData.position,
498 +                               cgColData.position);
499 +    
500 +    // if needed, gather the atomic rotation matrices
501 +    if (storageLayout_ & DataStorage::dslAmat) {
502 +      AtomCommMatrixRow->gather(snap_->atomData.aMat,
503 +                                atomRowData.aMat);
504 +      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
505 +                                   atomColData.aMat);
506 +    }
507 +    
508 +    // if needed, gather the atomic eletrostatic frames
509 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
510 +      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
511 +                                atomRowData.electroFrame);
512 +      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
513 +                                   atomColData.electroFrame);
514 +    }
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();
524 + #ifdef IS_MPI
525 +    
526 +    if (storageLayout_ & DataStorage::dslDensity) {
527 +      
528 +      AtomCommRealRow->scatter(atomRowData.density,
529 +                               snap_->atomData.density);
530 +      
531 +      int n = snap_->atomData.density.size();
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 +
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();
547 + #ifdef IS_MPI
548 +    if (storageLayout_ & DataStorage::dslFunctional) {
549 +      AtomCommRealRow->gather(snap_->atomData.functional,
550 +                              atomRowData.functional);
551 +      AtomCommRealColumn->gather(snap_->atomData.functional,
552 +                                 atomColData.functional);
553 +    }
554 +    
555 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
556 +      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
557 +                              atomRowData.functionalDerivative);
558 +      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
559 +                                 atomColData.functionalDerivative);
560 +    }
561 + #endif
562 +  }
563 +  
564 +  
565 +  void ForceMatrixDecomposition::collectData() {
566 +    snap_ = sman_->getCurrentSnapshot();
567 +    storageLayout_ = sman_->getStorageLayout();
568 + #ifdef IS_MPI    
569 +    int n = snap_->atomData.force.size();
570 +    vector<Vector3d> frc_tmp(n, V3Zero);
571 +    
572 +    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
573 +    for (int i = 0; i < n; i++) {
574 +      snap_->atomData.force[i] += frc_tmp[i];
575 +      frc_tmp[i] = 0.0;
576 +    }
577 +    
578 +    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
579 +    for (int i = 0; i < n; i++)
580 +      snap_->atomData.force[i] += frc_tmp[i];
581 +    
582 +    
583 +    if (storageLayout_ & DataStorage::dslTorque) {
584 +
585 +      int nt = snap_->atomData.force.size();
586 +      vector<Vector3d> trq_tmp(nt, V3Zero);
587 +
588 +      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
589 +      for (int i = 0; i < n; i++) {
590 +        snap_->atomData.torque[i] += trq_tmp[i];
591 +        trq_tmp[i] = 0.0;
592 +      }
593 +      
594 +      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
595 +      for (int i = 0; i < n; i++)
596 +        snap_->atomData.torque[i] += trq_tmp[i];
597 +    }
598 +    
599 +    nLocal_ = snap_->getNumberOfAtoms();
600 +
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;
651 +    
652 + #ifdef IS_MPI
653 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
654 + #else
655 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
656 + #endif
657 +    
658 +    snap_->wrapVector(d);
659 +    return d;    
660 +  }
661 +
662 +
663 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
664 +
665 +    Vector3d d;
666 +    
667 + #ifdef IS_MPI
668 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
669 + #else
670 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
671 + #endif
672 +
673 +    snap_->wrapVector(d);
674 +    return d;    
675 +  }
676 +  
677 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
678 +    Vector3d d;
679 +    
680 + #ifdef IS_MPI
681 +    d = cgColData.position[cg2] - atomColData.position[atom2];
682 + #else
683 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
684 + #endif
685 +    
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;
710 +    
711 + #ifdef IS_MPI
712 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
713 + #else
714 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
715 + #endif
716 +
717 +    snap_->wrapVector(d);
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;
767 + #else
768 +    snap_->atomData.force[atom1] += fg;
769 + #endif
770 +  }
771 +
772 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
773 + #ifdef IS_MPI
774 +    atomColData.force[atom2] += fg;
775 + #else
776 +    snap_->atomData.force[atom2] += fg;
777 + #endif
778 +  }
779 +
780 +    // filling interaction blocks with pointers
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 +    
793 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
794 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
795 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
796 +    }
797 +
798 +    if (storageLayout_ & DataStorage::dslTorque) {
799 +      idat.t1 = &(atomRowData.torque[atom1]);
800 +      idat.t2 = &(atomColData.torque[atom2]);
801 +    }
802 +
803 +    if (storageLayout_ & DataStorage::dslDensity) {
804 +      idat.rho1 = &(atomRowData.density[atom1]);
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]);
831 +    }
832 +
833 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
834 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
835 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
836 +    }
837 +
838 +    if (storageLayout_ & DataStorage::dslTorque) {
839 +      idat.t1 = &(snap_->atomData.torque[atom1]);
840 +      idat.t2 = &(snap_->atomData.torque[atom2]);
841 +    }
842 +
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
864 +  }
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 +    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 +
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 +
937 +  /*
938 +   * buildNeighborList
939 +   *
940 +   * first element of pair is row-indexed CutoffGroup
941 +   * second element of pair is column-indexed CutoffGroup
942 +   */
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 +    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_;
965 +
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 +
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 +    }
1004 +
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 + #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 +          int m1 = Vlinear(m1v, nCells_);
1061 +
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;          
1069 +            } else if (m2v.x() < 0) {
1070 +              m2v.x() = nCells_.x() - 1;
1071 +            }
1072 +            
1073 +            if (m2v.y() >= nCells_.y()) {
1074 +              m2v.y() = 0;          
1075 +            } else if (m2v.y() < 0) {
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 + #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 +  }
1142 + } //end namespace OpenMD

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