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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 1562 by gezelter, Thu May 12 17:00:14 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() {
54 >  void ForceMatrixDecomposition::distributeInitialData() {
55 >    snap_ = sman_->getCurrentSnapshot();
56 >    storageLayout_ = sman_->getStorageLayout();
57   #ifdef IS_MPI    
58 <    Snapshot* snap = sman_->getCurrentSnapshot();
59 <    int nLocal = snap->getNumberOfAtoms();
60 <    int nGroups = snap->getNumberOfCutoffGroups();
58 >    int nLocal = snap_->getNumberOfAtoms();
59 >    int nGroups = snap_->getNumberOfCutoffGroups();
60 >    
61 >    AtomCommIntRow = new Communicator<Row,int>(nLocal);
62 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
65  
66 <    AtomCommIntI = new Communicator<Row,int>(nLocal);
67 <    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
68 <    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
69 <    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
66 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
67 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
68 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
69 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
70  
71 <    AtomCommIntJ = new Communicator<Column,int>(nLocal);
72 <    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
73 <    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
74 <    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
71 >    cgCommIntRow = new Communicator<Row,int>(nGroups);
72 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
73 >    cgCommIntColumn = new Communicator<Column,int>(nGroups);
74 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
75  
76 <    cgCommIntI = new Communicator<Row,int>(nGroups);
77 <    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
78 <    cgCommIntJ = new Communicator<Column,int>(nGroups);
79 <    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
76 >    int nAtomsInRow = AtomCommIntRow->getSize();
77 >    int nAtomsInCol = AtomCommIntColumn->getSize();
78 >    int nGroupsInRow = cgCommIntRow->getSize();
79 >    int nGroupsInCol = cgCommIntColumn->getSize();
80  
81 <    int nAtomsInRow = AtomCommIntI->getSize();
82 <    int nAtomsInCol = AtomCommIntJ->getSize();
83 <    int nGroupsInRow = cgCommIntI->getSize();
84 <    int nGroupsInCol = cgCommIntJ->getSize();
85 <
81 >    // Modify the data storage objects with the correct layouts and sizes:
82 >    atomRowData.resize(nAtomsInRow);
83 >    atomRowData.setStorageLayout(storageLayout_);
84 >    atomColData.resize(nAtomsInCol);
85 >    atomColData.setStorageLayout(storageLayout_);
86 >    cgRowData.resize(nGroupsInRow);
87 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
88 >    cgColData.resize(nGroupsInCol);
89 >    cgColData.setStorageLayout(DataStorage::dslPosition);
90 >    
91      vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
92                                        vector<RealType> (nAtomsInRow, 0.0));
93      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94                                        vector<RealType> (nAtomsInCol, 0.0));
84 –    
85 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
95  
96 +
97 +    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
98 +    
99      // gather the information for atomtype IDs (atids):
100      vector<int> identsLocal = info_->getIdentArray();
101      identsRow.reserve(nAtomsInRow);
102      identsCol.reserve(nAtomsInCol);
103 +    
104 +    AtomCommIntRow->gather(identsLocal, identsRow);
105 +    AtomCommIntColumn->gather(identsLocal, identsCol);
106 +    
107 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
108 +    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109 +    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110 +    
111 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
112 +    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113 +    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
114  
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 –
115      // still need:
116      // topoDist
117      // exclude
# Line 110 | Line 120 | namespace OpenMD {
120      
121  
122  
123 <  void ForceDecomposition::distributeData()  {
123 >  void ForceMatrixDecomposition::distributeData()  {
124 >    snap_ = sman_->getCurrentSnapshot();
125 >    storageLayout_ = sman_->getStorageLayout();
126   #ifdef IS_MPI
115 –    Snapshot* snap = sman_->getCurrentSnapshot();
127      
128      // gather up the atomic positions
129 <    AtomCommVectorI->gather(snap->atomData.position,
130 <                            snap->atomIData.position);
131 <    AtomCommVectorJ->gather(snap->atomData.position,
132 <                            snap->atomJData.position);
129 >    AtomCommVectorRow->gather(snap_->atomData.position,
130 >                              atomRowData.position);
131 >    AtomCommVectorColumn->gather(snap_->atomData.position,
132 >                                 atomColData.position);
133      
134      // gather up the cutoff group positions
135 <    cgCommVectorI->gather(snap->cgData.position,
136 <                          snap->cgIData.position);
137 <    cgCommVectorJ->gather(snap->cgData.position,
138 <                          snap->cgJData.position);
135 >    cgCommVectorRow->gather(snap_->cgData.position,
136 >                            cgRowData.position);
137 >    cgCommVectorColumn->gather(snap_->cgData.position,
138 >                               cgColData.position);
139      
140      // if needed, gather the atomic rotation matrices
141 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
142 <      AtomCommMatrixI->gather(snap->atomData.aMat,
143 <                              snap->atomIData.aMat);
144 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
145 <                              snap->atomJData.aMat);
141 >    if (storageLayout_ & DataStorage::dslAmat) {
142 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
143 >                                atomRowData.aMat);
144 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
145 >                                   atomColData.aMat);
146      }
147      
148      // if needed, gather the atomic eletrostatic frames
149 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
150 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
151 <                              snap->atomIData.electroFrame);
152 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
153 <                              snap->atomJData.electroFrame);
149 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
150 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
151 >                                atomRowData.electroFrame);
152 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
153 >                                   atomColData.electroFrame);
154      }
155   #endif      
156    }
157    
158 <  void ForceDecomposition::collectIntermediateData() {
158 >  void ForceMatrixDecomposition::collectIntermediateData() {
159 >    snap_ = sman_->getCurrentSnapshot();
160 >    storageLayout_ = sman_->getStorageLayout();
161   #ifdef IS_MPI
149 –    Snapshot* snap = sman_->getCurrentSnapshot();
162      
163 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
164 <
165 <      AtomCommRealI->scatter(snap->atomIData.density,
166 <                             snap->atomData.density);
167 <
168 <      int n = snap->atomData.density.size();
163 >    if (storageLayout_ & DataStorage::dslDensity) {
164 >      
165 >      AtomCommRealRow->scatter(atomRowData.density,
166 >                               snap_->atomData.density);
167 >      
168 >      int n = snap_->atomData.density.size();
169        std::vector<RealType> rho_tmp(n, 0.0);
170 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
170 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
171        for (int i = 0; i < n; i++)
172 <        snap->atomData.density[i] += rho_tmp[i];
172 >        snap_->atomData.density[i] += rho_tmp[i];
173      }
174   #endif
175    }
176    
177 <  void ForceDecomposition::distributeIntermediateData() {
177 >  void ForceMatrixDecomposition::distributeIntermediateData() {
178 >    snap_ = sman_->getCurrentSnapshot();
179 >    storageLayout_ = sman_->getStorageLayout();
180   #ifdef IS_MPI
181 <    Snapshot* snap = sman_->getCurrentSnapshot();
182 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
183 <      AtomCommRealI->gather(snap->atomData.functional,
184 <                            snap->atomIData.functional);
185 <      AtomCommRealJ->gather(snap->atomData.functional,
172 <                            snap->atomJData.functional);
181 >    if (storageLayout_ & DataStorage::dslFunctional) {
182 >      AtomCommRealRow->gather(snap_->atomData.functional,
183 >                              atomRowData.functional);
184 >      AtomCommRealColumn->gather(snap_->atomData.functional,
185 >                                 atomColData.functional);
186      }
187      
188 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
189 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
190 <                            snap->atomIData.functionalDerivative);
191 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
192 <                            snap->atomJData.functionalDerivative);
188 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
189 >      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
190 >                              atomRowData.functionalDerivative);
191 >      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
192 >                                 atomColData.functionalDerivative);
193      }
194   #endif
195    }
196    
197    
198 <  void ForceDecomposition::collectData() {
199 < #ifdef IS_MPI
200 <    Snapshot* snap = sman_->getCurrentSnapshot();
201 <    
202 <    int n = snap->atomData.force.size();
198 >  void ForceMatrixDecomposition::collectData() {
199 >    snap_ = sman_->getCurrentSnapshot();
200 >    storageLayout_ = sman_->getStorageLayout();
201 > #ifdef IS_MPI    
202 >    int n = snap_->atomData.force.size();
203      vector<Vector3d> frc_tmp(n, V3Zero);
204      
205 <    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
205 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
206      for (int i = 0; i < n; i++) {
207 <      snap->atomData.force[i] += frc_tmp[i];
207 >      snap_->atomData.force[i] += frc_tmp[i];
208        frc_tmp[i] = 0.0;
209      }
210      
211 <    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
211 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
212      for (int i = 0; i < n; i++)
213 <      snap->atomData.force[i] += frc_tmp[i];
213 >      snap_->atomData.force[i] += frc_tmp[i];
214      
215      
216 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
216 >    if (storageLayout_ & DataStorage::dslTorque) {
217  
218 <      int nt = snap->atomData.force.size();
218 >      int nt = snap_->atomData.force.size();
219        vector<Vector3d> trq_tmp(nt, V3Zero);
220  
221 <      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
221 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
222        for (int i = 0; i < n; i++) {
223 <        snap->atomData.torque[i] += trq_tmp[i];
223 >        snap_->atomData.torque[i] += trq_tmp[i];
224          trq_tmp[i] = 0.0;
225        }
226        
227 <      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
227 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
228        for (int i = 0; i < n; i++)
229 <        snap->atomData.torque[i] += trq_tmp[i];
229 >        snap_->atomData.torque[i] += trq_tmp[i];
230      }
231      
232 <    int nLocal = snap->getNumberOfAtoms();
232 >    int nLocal = snap_->getNumberOfAtoms();
233  
234      vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
235                                         vector<RealType> (nLocal, 0.0));
236      
237      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
238 <      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
238 >      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
239        for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
240          pot_local[i] += pot_temp[i][ii];
241        }
242      }
243   #endif
244    }
245 +
246    
247 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
248 +    Vector3d d;
249 +    
250 + #ifdef IS_MPI
251 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
252 + #else
253 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
254 + #endif
255 +    
256 +    snap_->wrapVector(d);
257 +    return d;    
258 +  }
259 +
260 +
261 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
262 +
263 +    Vector3d d;
264 +    
265 + #ifdef IS_MPI
266 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
267 + #else
268 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
269 + #endif
270 +
271 +    snap_->wrapVector(d);
272 +    return d;    
273 +  }
274 +  
275 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
276 +    Vector3d d;
277 +    
278 + #ifdef IS_MPI
279 +    d = cgColData.position[cg2] - atomColData.position[atom2];
280 + #else
281 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
282 + #endif
283 +    
284 +    snap_->wrapVector(d);
285 +    return d;    
286 +  }
287 +    
288 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
289 +    Vector3d d;
290 +    
291 + #ifdef IS_MPI
292 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
293 + #else
294 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
295 + #endif
296 +
297 +    snap_->wrapVector(d);
298 +    return d;    
299 +  }
300 +
301 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
302 + #ifdef IS_MPI
303 +    atomRowData.force[atom1] += fg;
304 + #else
305 +    snap_->atomData.force[atom1] += fg;
306 + #endif
307 +  }
308 +
309 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
310 + #ifdef IS_MPI
311 +    atomColData.force[atom2] += fg;
312 + #else
313 +    snap_->atomData.force[atom2] += fg;
314 + #endif
315 +
316 +  }
317 +
318 +    // filling interaction blocks with pointers
319 +  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320 +
321 +    InteractionData idat;
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 +    
374 +  }
375 +  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
376 +    InteractionData idat;
377 +    skippedCharge1
378 +      skippedCharge2
379 +      rij
380 +      d
381 +    electroMult
382 +    sw
383 +    f
384 + #ifdef IS_MPI
385 +
386 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
387 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
388 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
389 +    }
390 +    if (storageLayout_ & DataStorage::dslTorque) {
391 +      idat.t1 = &(atomRowData.torque[atom1]);
392 +      idat.t2 = &(atomColData.torque[atom2]);
393 +    }
394 +
395 +    
396 +  }
397 +  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
398 +  }
399 +
400 +
401 +  /*
402 +   * buildNeighborList
403 +   *
404 +   * first element of pair is row-indexed CutoffGroup
405 +   * second element of pair is column-indexed CutoffGroup
406 +   */
407 +  vector<pair<int, int> >  buildNeighborList() {
408 +    Vector3d dr, invWid, rs, shift;
409 +    Vector3i cc, m1v, m2s;
410 +    RealType rrNebr;
411 +    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
412 +
413 +
414 +    vector<pair<int, int> > neighborList;  
415 +    Vector3i nCells;
416 +    Vector3d invWid, r;
417 +
418 +    rList_ = (rCut_ + skinThickness_);
419 +    rl2 = rList_ * rList_;
420 +
421 +    snap_ = sman_->getCurrentSnapshot();
422 +    Mat3x3d Hmat = snap_->getHmat();
423 +    Vector3d Hx = Hmat.getColumn(0);
424 +    Vector3d Hy = Hmat.getColumn(1);
425 +    Vector3d Hz = Hmat.getColumn(2);
426 +
427 +    nCells.x() = (int) ( Hx.length() )/ rList_;
428 +    nCells.y() = (int) ( Hy.length() )/ rList_;
429 +    nCells.z() = (int) ( Hz.length() )/ rList_;
430 +
431 +    for (i = 0; i < nGroupsInRow; i++) {
432 +      rs = cgRowData.position[i];
433 +      snap_->scaleVector(rs);    
434 +    }
435 +    
436 +
437 +    VDiv (invWid, cells, region);
438 +    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
439 +    for (n = 0; n < nMol; n ++) {
440 +      VSAdd (rs, mol[n].r, 0.5, region);
441 +      VMul (cc, rs, invWid);
442 +      c = VLinear (cc, cells) + nMol;
443 +      cellList[n] = cellList[c];
444 +      cellList[c] = n;
445 +    }
446 +    nebrTabLen = 0;
447 +    for (m1z = 0; m1z < cells.z(); m1z++) {
448 +      for (m1y = 0; m1y < cells.y(); m1y++) {
449 +        for (m1x = 0; m1x < cells.x(); m1x++) {
450 +          Vector3i m1v(m1x, m1y, m1z);
451 +          m1 = VLinear(m1v, cells) + nMol;
452 +          for (offset = 0; offset < nOffset_; offset++) {
453 +            m2v = m1v + cellOffsets_[offset];
454 +            shift = V3Zero();
455 +
456 +            if (m2v.x() >= cells.x) {
457 +              m2v.x() = 0;          
458 +              shift.x() = region.x();  
459 +            } else if (m2v.x() < 0) {
460 +              m2v.x() = cells.x() - 1;
461 +              shift.x() = - region.x();
462 +            }
463 +
464 +            if (m2v.y() >= cells.y()) {
465 +              m2v.y() = 0;          
466 +              shift.y() = region.y();  
467 +            } else if (m2v.y() < 0) {
468 +              m2v.y() = cells.y() - 1;
469 +              shift.y() = - region.y();
470 +            }
471 +
472 +            m2 = VLinear (m2v, cells) + nMol;
473 +            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
474 +              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
475 +                if (m1 != m2 || j2 < j1) {
476 +                  dr = mol[j1].r - mol[j2].r;
477 +                  VSub (dr, mol[j1].r, mol[j2].r);
478 +                  VVSub (dr, shift);
479 +                  if (VLenSq (dr) < rrNebr) {
480 +                    neighborList.push_back(make_pair(j1, j2));
481 +                  }
482 +                }
483 +              }
484 +            }
485 +          }
486 +        }
487 +      }
488 +    }
489 +  }
490 +
491 +  
492   } //end namespace OpenMD

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