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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1547 by gezelter, Mon Apr 11 18:44:16 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC

# Line 38 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 < #include "parallel/ForceDecomposition.hpp"
41 > #include "parallel/ForceMatrixDecomposition.hpp"
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
# Line 51 | Line 51 | namespace OpenMD {
51     * SimulationSetup
52     */
53    
54 <  void ForceDecomposition::distributeInitialData() {
55 < #ifdef IS_MPI    
56 <    Snapshot* snap = sman_->getCurrentSnapshot();
57 <    int nLocal = snap->getNumberOfAtoms();
58 <    int nGroups = snap->getNumberOfCutoffGroups();
54 >  void ForceMatrixDecomposition::distributeInitialData() {
55 >    snap_ = sman_->getCurrentSnapshot();
56 >    storageLayout_ = sman_->getStorageLayout();
57 >    nLocal_ = snap_->getNumberOfAtoms();
58 >    nGroups_ = snap_->getNumberOfCutoffGroups();
59  
60 <    AtomCommIntI = new Communicator<Row,int>(nLocal);
61 <    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
62 <    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
63 <    AtomCommMatrixI = 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 <    AtomCommIntJ = new Communicator<Column,int>(nLocal);
68 <    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
69 <    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
70 <    AtomCommMatrixJ = 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 <    cgCommIntI = new Communicator<Row,int>(nGroups);
73 <    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
74 <    cgCommIntJ = new Communicator<Column,int>(nGroups);
75 <    cgCommVectorJ = 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 = AtomCommIntI->getSize();
78 <    int nAtomsInCol = AtomCommIntJ->getSize();
79 <    int nGroupsInRow = cgCommIntI->getSize();
80 <    int nGroupsInCol = cgCommIntJ->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));
84 <    
85 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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);
107 >    
108 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
109 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
110 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
111 >    
112 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
113 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
114 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
115  
92 –    AtomCommIntI->gather(identsLocal, identsRow);
93 –    AtomCommIntJ->gather(identsLocal, identsCol);
94 –
95 –    AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
96 –    AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
97 –    AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
98 –
99 –    cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
100 –    cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
101 –    cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
102 –
103 –    
104 –
116      // still need:
117      // topoDist
118      // exclude
# Line 110 | Line 121 | namespace OpenMD {
121      
122  
123  
124 <  void ForceDecomposition::distributeData()  {
124 >  void ForceMatrixDecomposition::distributeData()  {
125 >    snap_ = sman_->getCurrentSnapshot();
126 >    storageLayout_ = sman_->getStorageLayout();
127   #ifdef IS_MPI
115 –    Snapshot* snap = sman_->getCurrentSnapshot();
128      
129      // gather up the atomic positions
130 <    AtomCommVectorI->gather(snap->atomData.position,
131 <                            snap->atomIData.position);
132 <    AtomCommVectorJ->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 <    cgCommVectorI->gather(snap->cgData.position,
137 <                          snap->cgIData.position);
138 <    cgCommVectorJ->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 <      AtomCommMatrixI->gather(snap->atomData.aMat,
144 <                              snap->atomIData.aMat);
145 <      AtomCommMatrixJ->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 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
152 <                              snap->atomIData.electroFrame);
153 <      AtomCommMatrixJ->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 ForceDecomposition::collectIntermediateData() {
159 >  void ForceMatrixDecomposition::collectIntermediateData() {
160 >    snap_ = sman_->getCurrentSnapshot();
161 >    storageLayout_ = sman_->getStorageLayout();
162   #ifdef IS_MPI
149 –    Snapshot* snap = sman_->getCurrentSnapshot();
163      
164 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
165 <
166 <      AtomCommRealI->scatter(snap->atomIData.density,
167 <                             snap->atomData.density);
168 <
169 <      int n = snap->atomData.density.size();
170 <      std::vector<RealType> rho_tmp(n, 0.0);
171 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
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(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 ForceDecomposition::distributeIntermediateData() {
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 <      AtomCommRealI->gather(snap->atomData.functional,
185 <                            snap->atomIData.functional);
186 <      AtomCommRealJ->gather(snap->atomData.functional,
172 <                            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 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
191 <                            snap->atomIData.functionalDerivative);
192 <      AtomCommRealJ->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 ForceDecomposition::collectData() {
200 < #ifdef IS_MPI
201 <    Snapshot* snap = sman_->getCurrentSnapshot();
202 <    
203 <    int n = snap->atomData.force.size();
199 >  void ForceMatrixDecomposition::collectData() {
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 <    AtomCommVectorI->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 <    AtomCommVectorJ->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 <      AtomCommVectorI->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 <      AtomCommVectorJ->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 <      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
239 >      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
240        for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
241          pot_local[i] += pot_temp[i][ii];
242        }
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 +
410 +
411 +
412 +  /*
413 +   * buildNeighborList
414 +   *
415 +   * first element of pair is row-indexed CutoffGroup
416 +   * second element of pair is column-indexed CutoffGroup
417 +   */
418 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
419 +      
420 +    vector<pair<int, int> > neighborList;
421 + #ifdef IS_MPI
422 +    cellListRow_.clear();
423 +    cellListCol_.clear();
424 + #else
425 +    cellList_.clear();
426 + #endif
427 +
428 +    // dangerous to not do error checking.
429 +    RealType rCut_;
430 +
431 +    RealType rList_ = (rCut_ + skinThickness_);
432 +    RealType rl2 = rList_ * rList_;
433 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
434 +    Mat3x3d Hmat = snap_->getHmat();
435 +    Vector3d Hx = Hmat.getColumn(0);
436 +    Vector3d Hy = Hmat.getColumn(1);
437 +    Vector3d Hz = Hmat.getColumn(2);
438 +
439 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
440 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
441 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
442 +
443 +    Mat3x3d invHmat = snap_->getInvHmat();
444 +    Vector3d rs, scaled, dr;
445 +    Vector3i whichCell;
446 +    int cellIndex;
447 +
448 + #ifdef IS_MPI
449 +    for (int i = 0; i < nGroupsInRow_; i++) {
450 +      rs = cgRowData.position[i];
451 +      // scaled positions relative to the box vectors
452 +      scaled = invHmat * rs;
453 +      // wrap the vector back into the unit box by subtracting integer box
454 +      // numbers
455 +      for (int j = 0; j < 3; j++)
456 +        scaled[j] -= roundMe(scaled[j]);
457 +    
458 +      // find xyz-indices of cell that cutoffGroup is in.
459 +      whichCell.x() = nCells_.x() * scaled.x();
460 +      whichCell.y() = nCells_.y() * scaled.y();
461 +      whichCell.z() = nCells_.z() * scaled.z();
462 +
463 +      // find single index of this cell:
464 +      cellIndex = Vlinear(whichCell, nCells_);
465 +      // add this cutoff group to the list of groups in this cell;
466 +      cellListRow_[cellIndex].push_back(i);
467 +    }
468 +
469 +    for (int i = 0; i < nGroupsInCol_; i++) {
470 +      rs = cgColData.position[i];
471 +      // scaled positions relative to the box vectors
472 +      scaled = invHmat * rs;
473 +      // wrap the vector back into the unit box by subtracting integer box
474 +      // numbers
475 +      for (int j = 0; j < 3; j++)
476 +        scaled[j] -= roundMe(scaled[j]);
477 +
478 +      // find xyz-indices of cell that cutoffGroup is in.
479 +      whichCell.x() = nCells_.x() * scaled.x();
480 +      whichCell.y() = nCells_.y() * scaled.y();
481 +      whichCell.z() = nCells_.z() * scaled.z();
482 +
483 +      // find single index of this cell:
484 +      cellIndex = Vlinear(whichCell, nCells_);
485 +      // add this cutoff group to the list of groups in this cell;
486 +      cellListCol_[cellIndex].push_back(i);
487 +    }
488 + #else
489 +    for (int i = 0; i < nGroups_; i++) {
490 +      rs = snap_->cgData.position[i];
491 +      // scaled positions relative to the box vectors
492 +      scaled = invHmat * rs;
493 +      // wrap the vector back into the unit box by subtracting integer box
494 +      // numbers
495 +      for (int j = 0; j < 3; j++)
496 +        scaled[j] -= roundMe(scaled[j]);
497 +
498 +      // find xyz-indices of cell that cutoffGroup is in.
499 +      whichCell.x() = nCells_.x() * scaled.x();
500 +      whichCell.y() = nCells_.y() * scaled.y();
501 +      whichCell.z() = nCells_.z() * scaled.z();
502 +
503 +      // find single index of this cell:
504 +      cellIndex = Vlinear(whichCell, nCells_);
505 +      // add this cutoff group to the list of groups in this cell;
506 +      cellList_[cellIndex].push_back(i);
507 +    }
508 + #endif
509 +
510 +
511 +
512 +    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
513 +      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
514 +        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
515 +          Vector3i m1v(m1x, m1y, m1z);
516 +          int m1 = Vlinear(m1v, nCells_);
517 +
518 +          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
519 +               os != cellOffsets_.end(); ++os) {
520 +            
521 +            Vector3i m2v = m1v + (*os);
522 +            
523 +            if (m2v.x() >= nCells_.x()) {
524 +              m2v.x() = 0;          
525 +            } else if (m2v.x() < 0) {
526 +              m2v.x() = nCells_.x() - 1;
527 +            }
528 +            
529 +            if (m2v.y() >= nCells_.y()) {
530 +              m2v.y() = 0;          
531 +            } else if (m2v.y() < 0) {
532 +              m2v.y() = nCells_.y() - 1;
533 +            }
534 +            
535 +            if (m2v.z() >= nCells_.z()) {
536 +              m2v.z() = 0;          
537 +            } else if (m2v.z() < 0) {
538 +              m2v.z() = nCells_.z() - 1;
539 +            }
540 +            
541 +            int m2 = Vlinear (m2v, nCells_);
542 +
543 + #ifdef IS_MPI
544 +            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
545 +                 j1 != cellListRow_[m1].end(); ++j1) {
546 +              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
547 +                   j2 != cellListCol_[m2].end(); ++j2) {
548 +                              
549 +                // Always do this if we're in different cells or if
550 +                // we're in the same cell and the global index of the
551 +                // j2 cutoff group is less than the j1 cutoff group
552 +
553 +                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
554 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
555 +                  snap_->wrapVector(dr);
556 +                  if (dr.lengthSquare() < rl2) {
557 +                    neighborList.push_back(make_pair((*j1), (*j2)));
558 +                  }
559 +                }
560 +              }
561 +            }
562 + #else
563 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
564 +                 j1 != cellList_[m1].end(); ++j1) {
565 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
566 +                   j2 != cellList_[m2].end(); ++j2) {
567 +                              
568 +                // Always do this if we're in different cells or if
569 +                // we're in the same cell and the global index of the
570 +                // j2 cutoff group is less than the j1 cutoff group
571 +
572 +                if (m2 != m1 || (*j2) < (*j1)) {
573 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
574 +                  snap_->wrapVector(dr);
575 +                  if (dr.lengthSquare() < rl2) {
576 +                    neighborList.push_back(make_pair((*j1), (*j2)));
577 +                  }
578 +                }
579 +              }
580 +            }
581 + #endif
582 +          }
583 +        }
584 +      }
585 +    }
586 +
587 +    // save the local cutoff group positions for the check that is
588 +    // done on each loop:
589 +    saved_CG_positions_.clear();
590 +    for (int i = 0; i < nGroups_; i++)
591 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
592 +
593 +    return neighborList;
594 +  }
595   } //end namespace OpenMD

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