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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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC

# Line 52 | Line 52 | namespace OpenMD {
52     */
53    
54    void ForceMatrixDecomposition::distributeInitialData() {
55 < #ifdef IS_MPI    
56 <    Snapshot* snap = sman_->getCurrentSnapshot();
57 <    int nLocal = snap->getNumberOfAtoms();
58 <    int nGroups = snap->getNumberOfCutoffGroups();
55 >    snap_ = sman_->getCurrentSnapshot();
56 >    storageLayout_ = sman_->getStorageLayout();
57 >    nLocal_ = snap_->getNumberOfAtoms();
58 >    nGroups_ = snap_->getNumberOfCutoffGroups();
59  
60 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
61 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
62 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
63 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
60 > #ifdef IS_MPI
61 >
62 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
63 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
66  
67 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
68 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
69 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
70 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
67 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
68 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
69 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
70 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
71  
72 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
73 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
74 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
75 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
72 >    cgCommIntRow = new Communicator<Row,int>(nGroups_);
73 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
74 >    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
75 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
76  
77 <    int nAtomsInRow = AtomCommIntRow->getSize();
78 <    int nAtomsInCol = AtomCommIntColumn->getSize();
79 <    int nGroupsInRow = cgCommIntRow->getSize();
80 <    int nGroupsInCol = cgCommIntColumn->getSize();
77 >    nAtomsInRow_ = AtomCommIntRow->getSize();
78 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
79 >    nGroupsInRow_ = cgCommIntRow->getSize();
80 >    nGroupsInCol_ = cgCommIntColumn->getSize();
81 >
82 >    // Modify the data storage objects with the correct layouts and sizes:
83 >    atomRowData.resize(nAtomsInRow_);
84 >    atomRowData.setStorageLayout(storageLayout_);
85 >    atomColData.resize(nAtomsInCol_);
86 >    atomColData.setStorageLayout(storageLayout_);
87 >    cgRowData.resize(nGroupsInRow_);
88 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
89 >    cgColData.resize(nGroupsInCol_);
90 >    cgColData.setStorageLayout(DataStorage::dslPosition);
91      
92      vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
93 <                                      vector<RealType> (nAtomsInRow, 0.0));
93 >                                      vector<RealType> (nAtomsInRow_, 0.0));
94      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95 <                                      vector<RealType> (nAtomsInCol, 0.0));
96 <    
95 >                                      vector<RealType> (nAtomsInCol_, 0.0));
96 >
97 >
98      vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
99      
100      // gather the information for atomtype IDs (atids):
101      vector<int> identsLocal = info_->getIdentArray();
102 <    identsRow.reserve(nAtomsInRow);
103 <    identsCol.reserve(nAtomsInCol);
102 >    identsRow.reserve(nAtomsInRow_);
103 >    identsCol.reserve(nAtomsInCol_);
104      
105      AtomCommIntRow->gather(identsLocal, identsRow);
106      AtomCommIntColumn->gather(identsLocal, identsCol);
# Line 109 | Line 122 | namespace OpenMD {
122  
123  
124    void ForceMatrixDecomposition::distributeData()  {
125 +    snap_ = sman_->getCurrentSnapshot();
126 +    storageLayout_ = sman_->getStorageLayout();
127   #ifdef IS_MPI
113 –    Snapshot* snap = sman_->getCurrentSnapshot();
128      
129      // gather up the atomic positions
130 <    AtomCommVectorRow->gather(snap->atomData.position,
131 <                            snap->atomIData.position);
132 <    AtomCommVectorColumn->gather(snap->atomData.position,
133 <                            snap->atomJData.position);
130 >    AtomCommVectorRow->gather(snap_->atomData.position,
131 >                              atomRowData.position);
132 >    AtomCommVectorColumn->gather(snap_->atomData.position,
133 >                                 atomColData.position);
134      
135      // gather up the cutoff group positions
136 <    cgCommVectorRow->gather(snap->cgData.position,
137 <                          snap->cgIData.position);
138 <    cgCommVectorColumn->gather(snap->cgData.position,
139 <                          snap->cgJData.position);
136 >    cgCommVectorRow->gather(snap_->cgData.position,
137 >                            cgRowData.position);
138 >    cgCommVectorColumn->gather(snap_->cgData.position,
139 >                               cgColData.position);
140      
141      // if needed, gather the atomic rotation matrices
142 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
143 <      AtomCommMatrixRow->gather(snap->atomData.aMat,
144 <                              snap->atomIData.aMat);
145 <      AtomCommMatrixColumn->gather(snap->atomData.aMat,
146 <                              snap->atomJData.aMat);
142 >    if (storageLayout_ & DataStorage::dslAmat) {
143 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
144 >                                atomRowData.aMat);
145 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
146 >                                   atomColData.aMat);
147      }
148      
149      // if needed, gather the atomic eletrostatic frames
150 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
151 <      AtomCommMatrixRow->gather(snap->atomData.electroFrame,
152 <                              snap->atomIData.electroFrame);
153 <      AtomCommMatrixColumn->gather(snap->atomData.electroFrame,
154 <                              snap->atomJData.electroFrame);
150 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
151 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
152 >                                atomRowData.electroFrame);
153 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
154 >                                   atomColData.electroFrame);
155      }
156   #endif      
157    }
158    
159    void ForceMatrixDecomposition::collectIntermediateData() {
160 +    snap_ = sman_->getCurrentSnapshot();
161 +    storageLayout_ = sman_->getStorageLayout();
162   #ifdef IS_MPI
147 –    Snapshot* snap = sman_->getCurrentSnapshot();
163      
164 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
165 <
166 <      AtomCommRealRow->scatter(snap->atomIData.density,
167 <                             snap->atomData.density);
168 <
169 <      int n = snap->atomData.density.size();
164 >    if (storageLayout_ & DataStorage::dslDensity) {
165 >      
166 >      AtomCommRealRow->scatter(atomRowData.density,
167 >                               snap_->atomData.density);
168 >      
169 >      int n = snap_->atomData.density.size();
170        std::vector<RealType> rho_tmp(n, 0.0);
171 <      AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp);
171 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
172        for (int i = 0; i < n; i++)
173 <        snap->atomData.density[i] += rho_tmp[i];
173 >        snap_->atomData.density[i] += rho_tmp[i];
174      }
175   #endif
176    }
177    
178    void ForceMatrixDecomposition::distributeIntermediateData() {
179 +    snap_ = sman_->getCurrentSnapshot();
180 +    storageLayout_ = sman_->getStorageLayout();
181   #ifdef IS_MPI
182 <    Snapshot* snap = sman_->getCurrentSnapshot();
183 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
184 <      AtomCommRealRow->gather(snap->atomData.functional,
185 <                            snap->atomIData.functional);
186 <      AtomCommRealColumn->gather(snap->atomData.functional,
170 <                            snap->atomJData.functional);
182 >    if (storageLayout_ & DataStorage::dslFunctional) {
183 >      AtomCommRealRow->gather(snap_->atomData.functional,
184 >                              atomRowData.functional);
185 >      AtomCommRealColumn->gather(snap_->atomData.functional,
186 >                                 atomColData.functional);
187      }
188      
189 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
190 <      AtomCommRealRow->gather(snap->atomData.functionalDerivative,
191 <                            snap->atomIData.functionalDerivative);
192 <      AtomCommRealColumn->gather(snap->atomData.functionalDerivative,
193 <                            snap->atomJData.functionalDerivative);
189 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
190 >      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
191 >                              atomRowData.functionalDerivative);
192 >      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
193 >                                 atomColData.functionalDerivative);
194      }
195   #endif
196    }
197    
198    
199    void ForceMatrixDecomposition::collectData() {
200 < #ifdef IS_MPI
201 <    Snapshot* snap = sman_->getCurrentSnapshot();
202 <    
203 <    int n = snap->atomData.force.size();
200 >    snap_ = sman_->getCurrentSnapshot();
201 >    storageLayout_ = sman_->getStorageLayout();
202 > #ifdef IS_MPI    
203 >    int n = snap_->atomData.force.size();
204      vector<Vector3d> frc_tmp(n, V3Zero);
205      
206 <    AtomCommVectorRow->scatter(snap->atomIData.force, frc_tmp);
206 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
207      for (int i = 0; i < n; i++) {
208 <      snap->atomData.force[i] += frc_tmp[i];
208 >      snap_->atomData.force[i] += frc_tmp[i];
209        frc_tmp[i] = 0.0;
210      }
211      
212 <    AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
212 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
213      for (int i = 0; i < n; i++)
214 <      snap->atomData.force[i] += frc_tmp[i];
214 >      snap_->atomData.force[i] += frc_tmp[i];
215      
216      
217 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
217 >    if (storageLayout_ & DataStorage::dslTorque) {
218  
219 <      int nt = snap->atomData.force.size();
219 >      int nt = snap_->atomData.force.size();
220        vector<Vector3d> trq_tmp(nt, V3Zero);
221  
222 <      AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp);
222 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
223        for (int i = 0; i < n; i++) {
224 <        snap->atomData.torque[i] += trq_tmp[i];
224 >        snap_->atomData.torque[i] += trq_tmp[i];
225          trq_tmp[i] = 0.0;
226        }
227        
228 <      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
228 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
229        for (int i = 0; i < n; i++)
230 <        snap->atomData.torque[i] += trq_tmp[i];
230 >        snap_->atomData.torque[i] += trq_tmp[i];
231      }
232      
233 <    int nLocal = snap->getNumberOfAtoms();
233 >    nLocal_ = snap_->getNumberOfAtoms();
234  
235      vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
236 <                                       vector<RealType> (nLocal, 0.0));
236 >                                       vector<RealType> (nLocal_, 0.0));
237      
238      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
239        AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
# Line 227 | Line 243 | namespace OpenMD {
243      }
244   #endif
245    }
246 +
247    
248 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
249 +    Vector3d d;
250 +    
251 + #ifdef IS_MPI
252 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
253 + #else
254 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
255 + #endif
256 +    
257 +    snap_->wrapVector(d);
258 +    return d;    
259 +  }
260 +
261 +
262 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
263 +
264 +    Vector3d d;
265 +    
266 + #ifdef IS_MPI
267 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
268 + #else
269 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
270 + #endif
271 +
272 +    snap_->wrapVector(d);
273 +    return d;    
274 +  }
275 +  
276 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
277 +    Vector3d d;
278 +    
279 + #ifdef IS_MPI
280 +    d = cgColData.position[cg2] - atomColData.position[atom2];
281 + #else
282 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
283 + #endif
284 +    
285 +    snap_->wrapVector(d);
286 +    return d;    
287 +  }
288 +    
289 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
290 +    Vector3d d;
291 +    
292 + #ifdef IS_MPI
293 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
294 + #else
295 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
296 + #endif
297 +
298 +    snap_->wrapVector(d);
299 +    return d;    
300 +  }
301 +
302 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
303 + #ifdef IS_MPI
304 +    atomRowData.force[atom1] += fg;
305 + #else
306 +    snap_->atomData.force[atom1] += fg;
307 + #endif
308 +  }
309 +
310 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
311 + #ifdef IS_MPI
312 +    atomColData.force[atom2] += fg;
313 + #else
314 +    snap_->atomData.force[atom2] += fg;
315 + #endif
316 +  }
317 +
318 +    // filling interaction blocks with pointers
319 +  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320 +    InteractionData idat;
321 +
322 + #ifdef IS_MPI
323 +    if (storageLayout_ & DataStorage::dslAmat) {
324 +      idat.A1 = &(atomRowData.aMat[atom1]);
325 +      idat.A2 = &(atomColData.aMat[atom2]);
326 +    }
327 +    
328 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
329 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
330 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
331 +    }
332 +
333 +    if (storageLayout_ & DataStorage::dslTorque) {
334 +      idat.t1 = &(atomRowData.torque[atom1]);
335 +      idat.t2 = &(atomColData.torque[atom2]);
336 +    }
337 +
338 +    if (storageLayout_ & DataStorage::dslDensity) {
339 +      idat.rho1 = &(atomRowData.density[atom1]);
340 +      idat.rho2 = &(atomColData.density[atom2]);
341 +    }
342 +
343 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
344 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
345 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
346 +    }
347 + #else
348 +    if (storageLayout_ & DataStorage::dslAmat) {
349 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
350 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
351 +    }
352 +
353 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
354 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
355 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
356 +    }
357 +
358 +    if (storageLayout_ & DataStorage::dslTorque) {
359 +      idat.t1 = &(snap_->atomData.torque[atom1]);
360 +      idat.t2 = &(snap_->atomData.torque[atom2]);
361 +    }
362 +
363 +    if (storageLayout_ & DataStorage::dslDensity) {
364 +      idat.rho1 = &(snap_->atomData.density[atom1]);
365 +      idat.rho2 = &(snap_->atomData.density[atom2]);
366 +    }
367 +
368 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
369 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
370 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
371 +    }
372 + #endif
373 +    return idat;
374 +  }
375 +
376 +  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
377 +
378 +    InteractionData idat;
379 + #ifdef IS_MPI
380 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
381 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
382 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
383 +    }
384 +    if (storageLayout_ & DataStorage::dslTorque) {
385 +      idat.t1 = &(atomRowData.torque[atom1]);
386 +      idat.t2 = &(atomColData.torque[atom2]);
387 +    }
388 +    if (storageLayout_ & DataStorage::dslForce) {
389 +      idat.t1 = &(atomRowData.force[atom1]);
390 +      idat.t2 = &(atomColData.force[atom2]);
391 +    }
392 + #else
393 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
394 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
395 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
396 +    }
397 +    if (storageLayout_ & DataStorage::dslTorque) {
398 +      idat.t1 = &(snap_->atomData.torque[atom1]);
399 +      idat.t2 = &(snap_->atomData.torque[atom2]);
400 +    }
401 +    if (storageLayout_ & DataStorage::dslForce) {
402 +      idat.t1 = &(snap_->atomData.force[atom1]);
403 +      idat.t2 = &(snap_->atomData.force[atom2]);
404 +    }
405 + #endif
406 +    
407 +  }
408 +
409 +  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
410 +    SelfData sdat;
411 +    // Still Missing atype, skippedCharge, potVec pot,
412 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
413 +      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
414 +    }
415 +    
416 +    if (storageLayout_ & DataStorage::dslTorque) {
417 +      sdat.t = &(snap_->atomData.torque[atom1]);
418 +    }
419 +    
420 +    if (storageLayout_ & DataStorage::dslDensity) {
421 +      sdat.rho = &(snap_->atomData.density[atom1]);
422 +    }
423 +    
424 +    if (storageLayout_ & DataStorage::dslFunctional) {
425 +      sdat.frho = &(snap_->atomData.functional[atom1]);
426 +    }
427 +    
428 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429 +      sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430 +    }
431 +
432 +    return sdat;    
433 +  }
434 +
435 +
436 +
437 +  /*
438 +   * buildNeighborList
439 +   *
440 +   * first element of pair is row-indexed CutoffGroup
441 +   * second element of pair is column-indexed CutoffGroup
442 +   */
443 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
444 +      
445 +    vector<pair<int, int> > neighborList;
446 + #ifdef IS_MPI
447 +    CellListRow.clear();
448 +    CellListCol.clear();
449 + #else
450 +    CellList.clear();
451 + #endif
452 +
453 +    // dangerous to not do error checking.
454 +    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455 +    RealType rCut_;
456 +
457 +    RealType rList_ = (rCut_ + skinThickness_);
458 +    RealType rl2 = rList_ * rList_;
459 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
460 +    Mat3x3d Hmat = snap_->getHmat();
461 +    Vector3d Hx = Hmat.getColumn(0);
462 +    Vector3d Hy = Hmat.getColumn(1);
463 +    Vector3d Hz = Hmat.getColumn(2);
464 +    Vector3i nCells;
465 +
466 +    nCells.x() = (int) ( Hx.length() )/ rList_;
467 +    nCells.y() = (int) ( Hy.length() )/ rList_;
468 +    nCells.z() = (int) ( Hz.length() )/ rList_;
469 +
470 +    Mat3x3d invHmat = snap_->getInvHmat();
471 +    Vector3d rs, scaled, dr;
472 +    Vector3i whichCell;
473 +    int cellIndex;
474 +
475 + #ifdef IS_MPI
476 +    for (int i = 0; i < nGroupsInRow_; i++) {
477 +      rs = cgRowData.position[i];
478 +      // scaled positions relative to the box vectors
479 +      scaled = invHmat * rs;
480 +      // wrap the vector back into the unit box by subtracting integer box
481 +      // numbers
482 +      for (int j = 0; j < 3; j++)
483 +        scaled[j] -= roundMe(scaled[j]);
484 +    
485 +      // find xyz-indices of cell that cutoffGroup is in.
486 +      whichCell.x() = nCells.x() * scaled.x();
487 +      whichCell.y() = nCells.y() * scaled.y();
488 +      whichCell.z() = nCells.z() * scaled.z();
489 +
490 +      // find single index of this cell:
491 +      cellIndex = Vlinear(whichCell, nCells);
492 +      // add this cutoff group to the list of groups in this cell;
493 +      CellListRow[cellIndex].push_back(i);
494 +    }
495 +
496 +    for (int i = 0; i < nGroupsInCol_; i++) {
497 +      rs = cgColData.position[i];
498 +      // scaled positions relative to the box vectors
499 +      scaled = invHmat * rs;
500 +      // wrap the vector back into the unit box by subtracting integer box
501 +      // numbers
502 +      for (int j = 0; j < 3; j++)
503 +        scaled[j] -= roundMe(scaled[j]);
504 +
505 +      // find xyz-indices of cell that cutoffGroup is in.
506 +      whichCell.x() = nCells.x() * scaled.x();
507 +      whichCell.y() = nCells.y() * scaled.y();
508 +      whichCell.z() = nCells.z() * scaled.z();
509 +
510 +      // find single index of this cell:
511 +      cellIndex = Vlinear(whichCell, nCells);
512 +      // add this cutoff group to the list of groups in this cell;
513 +      CellListCol[cellIndex].push_back(i);
514 +    }
515 + #else
516 +    for (int i = 0; i < nGroups_; i++) {
517 +      rs = snap_->cgData.position[i];
518 +      // scaled positions relative to the box vectors
519 +      scaled = invHmat * rs;
520 +      // wrap the vector back into the unit box by subtracting integer box
521 +      // numbers
522 +      for (int j = 0; j < 3; j++)
523 +        scaled[j] -= roundMe(scaled[j]);
524 +
525 +      // find xyz-indices of cell that cutoffGroup is in.
526 +      whichCell.x() = nCells.x() * scaled.x();
527 +      whichCell.y() = nCells.y() * scaled.y();
528 +      whichCell.z() = nCells.z() * scaled.z();
529 +
530 +      // find single index of this cell:
531 +      cellIndex = Vlinear(whichCell, nCells);
532 +      // add this cutoff group to the list of groups in this cell;
533 +      CellList[cellIndex].push_back(i);
534 +    }
535 + #endif
536 +
537 +
538 +
539 +    for (int m1z = 0; m1z < nCells.z(); m1z++) {
540 +      for (int m1y = 0; m1y < nCells.y(); m1y++) {
541 +        for (int m1x = 0; m1x < nCells.x(); m1x++) {
542 +          Vector3i m1v(m1x, m1y, m1z);
543 +          int m1 = Vlinear(m1v, nCells);
544 +          for (int offset = 0; offset < nOffset_; offset++) {
545 +            Vector3i m2v = m1v + cellOffsets_[offset];
546 +
547 +            if (m2v.x() >= nCells.x()) {
548 +              m2v.x() = 0;          
549 +            } else if (m2v.x() < 0) {
550 +              m2v.x() = nCells.x() - 1;
551 +            }
552 +
553 +            if (m2v.y() >= nCells.y()) {
554 +              m2v.y() = 0;          
555 +            } else if (m2v.y() < 0) {
556 +              m2v.y() = nCells.y() - 1;
557 +            }
558 +
559 +            if (m2v.z() >= nCells.z()) {
560 +              m2v.z() = 0;          
561 +            } else if (m2v.z() < 0) {
562 +              m2v.z() = nCells.z() - 1;
563 +            }
564 +
565 +            int m2 = Vlinear (m2v, nCells);
566 +
567 + #ifdef IS_MPI
568 +            for (vector<int>::iterator j1 = CellListRow[m1].begin();
569 +                 j1 != CellListRow[m1].end(); ++j1) {
570 +              for (vector<int>::iterator j2 = CellListCol[m2].begin();
571 +                   j2 != CellListCol[m2].end(); ++j2) {
572 +                              
573 +                // Always do this if we're in different cells or if
574 +                // we're in the same cell and the global index of the
575 +                // j2 cutoff group is less than the j1 cutoff group
576 +
577 +                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
578 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
579 +                  snap_->wrapVector(dr);
580 +                  if (dr.lengthSquare() < rl2) {
581 +                    neighborList.push_back(make_pair((*j1), (*j2)));
582 +                  }
583 +                }
584 +              }
585 +            }
586 + #else
587 +            for (vector<int>::iterator j1 = CellList[m1].begin();
588 +                 j1 != CellList[m1].end(); ++j1) {
589 +              for (vector<int>::iterator j2 = CellList[m2].begin();
590 +                   j2 != CellList[m2].end(); ++j2) {
591 +                              
592 +                // Always do this if we're in different cells or if
593 +                // we're in the same cell and the global index of the
594 +                // j2 cutoff group is less than the j1 cutoff group
595 +
596 +                if (m2 != m1 || (*j2) < (*j1)) {
597 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
598 +                  snap_->wrapVector(dr);
599 +                  if (dr.lengthSquare() < rl2) {
600 +                    neighborList.push_back(make_pair((*j1), (*j2)));
601 +                  }
602 +                }
603 +              }
604 +            }
605 + #endif
606 +          }
607 +        }
608 +      }
609 +    }
610 +    return neighborList;
611 +  }
612   } //end namespace OpenMD

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