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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62      // gather the information for atomtype IDs (atids):
63      identsLocal = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
# Line 104 | Line 104 | namespace OpenMD {
104      cgColData.resize(nGroupsInCol_);
105      cgColData.setStorageLayout(DataStorage::dslPosition);
106          
107 <    identsRow.reserve(nAtomsInRow_);
108 <    identsCol.reserve(nAtomsInCol_);
107 >    identsRow.resize(nAtomsInRow_);
108 >    identsCol.resize(nAtomsInCol_);
109      
110      AtomCommIntRow->gather(identsLocal, identsRow);
111      AtomCommIntColumn->gather(identsLocal, identsCol);
# Line 120 | Line 120 | namespace OpenMD {
120      AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121  
122      groupListRow_.clear();
123 <    groupListRow_.reserve(nGroupsInRow_);
123 >    groupListRow_.resize(nGroupsInRow_);
124      for (int i = 0; i < nGroupsInRow_; i++) {
125        int gid = cgRowToGlobal[i];
126        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 131 | namespace OpenMD {
131      }
132  
133      groupListCol_.clear();
134 <    groupListCol_.reserve(nGroupsInCol_);
134 >    groupListCol_.resize(nGroupsInCol_);
135      for (int i = 0; i < nGroupsInCol_; i++) {
136        int gid = cgColToGlobal[i];
137        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 142 | Line 142 | namespace OpenMD {
142      }
143  
144      skipsForRowAtom.clear();
145 <    skipsForRowAtom.reserve(nAtomsInRow_);
145 >    skipsForRowAtom.resize(nAtomsInRow_);
146      for (int i = 0; i < nAtomsInRow_; i++) {
147        int iglob = AtomRowToGlobal[i];
148        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 153 | Line 153 | namespace OpenMD {
153      }
154  
155      toposForRowAtom.clear();
156 <    toposForRowAtom.reserve(nAtomsInRow_);
156 >    toposForRowAtom.resize(nAtomsInRow_);
157      for (int i = 0; i < nAtomsInRow_; i++) {
158        int iglob = AtomRowToGlobal[i];
159        int nTopos = 0;
# Line 178 | Line 178 | namespace OpenMD {
178      }
179  
180   #endif
181 –
181      groupList_.clear();
182 <    groupList_.reserve(nGroups_);
182 >    groupList_.resize(nGroups_);
183      for (int i = 0; i < nGroups_; i++) {
184        int gid = cgLocalToGlobal[i];
185        for (int j = 0; j < nLocal_; j++) {
186          int aid = AtomLocalToGlobal[j];
187 <        if (globalGroupMembership[aid] == gid)
187 >        if (globalGroupMembership[aid] == gid) {
188            groupList_[i].push_back(j);
189 +
190 +        }
191        }      
192      }
193  
194      skipsForLocalAtom.clear();
195 <    skipsForLocalAtom.reserve(nLocal_);
195 >    skipsForLocalAtom.resize(nLocal_);
196  
197      for (int i = 0; i < nLocal_; i++) {
198        int iglob = AtomLocalToGlobal[i];
# Line 201 | Line 202 | namespace OpenMD {
202            skipsForLocalAtom[i].push_back(j);      
203        }      
204      }
204 –
205      toposForLocalAtom.clear();
206 <    toposForLocalAtom.reserve(nLocal_);
206 >    toposForLocalAtom.resize(nLocal_);
207      for (int i = 0; i < nLocal_; i++) {
208        int iglob = AtomLocalToGlobal[i];
209        int nTopos = 0;
# Line 225 | Line 225 | namespace OpenMD {
225            nTopos++;
226          }
227        }      
228 <    }
228 >    }    
229 >
230    }
231    
232 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
233 +
234 +    RealType tol = 1e-6;
235 +    RealType rc;
236 +    int atid;
237 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
238 +    vector<RealType> atypeCutoff;
239 +    atypeCutoff.resize( atypes.size() );
240 +
241 +    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
242 +      rc = interactionMan_->getSuggestedCutoffRadius(*at);
243 +      atid = (*at)->getIdent();
244 +      atypeCutoff[atid] = rc;
245 +    }
246 +
247 +    vector<RealType> gTypeCutoffs;
248 +
249 +    // first we do a single loop over the cutoff groups to find the
250 +    // largest cutoff for any atypes present in this group.
251 + #ifdef IS_MPI
252 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
254 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
255 +      for (vector<int>::iterator ia = atomListRow.begin();
256 +           ia != atomListRow.end(); ++ia) {            
257 +        int atom1 = (*ia);
258 +        atid = identsRow[atom1];
259 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
260 +          groupCutoffRow[cg1] = atypeCutoff[atid];
261 +        }
262 +      }
263 +
264 +      bool gTypeFound = false;
265 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
266 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
267 +          groupRowToGtype[cg1] = gt;
268 +          gTypeFound = true;
269 +        }
270 +      }
271 +      if (!gTypeFound) {
272 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
273 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
274 +      }
275 +      
276 +    }
277 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
278 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280 +      for (vector<int>::iterator jb = atomListCol.begin();
281 +           jb != atomListCol.end(); ++jb) {            
282 +        int atom2 = (*jb);
283 +        atid = identsCol[atom2];
284 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
285 +          groupCutoffCol[cg2] = atypeCutoff[atid];
286 +        }
287 +      }
288 +      bool gTypeFound = false;
289 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
290 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
291 +          groupColToGtype[cg2] = gt;
292 +          gTypeFound = true;
293 +        }
294 +      }
295 +      if (!gTypeFound) {
296 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
297 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
298 +      }
299 +    }
300 + #else
301 +    vector<RealType> groupCutoff(nGroups_, 0.0);
302 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
303 +      groupCutoff[cg1] = 0.0;
304 +      vector<int> atomList = getAtomsInGroupRow(cg1);
305 +      for (vector<int>::iterator ia = atomList.begin();
306 +           ia != atomList.end(); ++ia) {            
307 +        int atom1 = (*ia);
308 +        atid = identsLocal[atom1];
309 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
310 +          groupCutoff[cg1] = atypeCutoff[atid];
311 +        }
312 +      }
313 +
314 +      bool gTypeFound = false;
315 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
316 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
317 +          groupToGtype[cg1] = gt;
318 +          gTypeFound = true;
319 +        }
320 +      }
321 +      if (!gTypeFound) {
322 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
323 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
324 +      }      
325 +    }
326 + #endif
327 +
328 +    // Now we find the maximum group cutoff value present in the simulation
329 +
330 +    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331 +    RealType groupMax = *groupMaxLoc;
332 +
333 + #ifdef IS_MPI
334 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
335 + #endif
336 +    
337 +    RealType tradRcut = groupMax;
338 +
339 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
340 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 +        
342 +        RealType thisRcut;
343 +        switch(cutoffPolicy_) {
344 +        case TRADITIONAL:
345 +          thisRcut = tradRcut;
346 +        case MIX:
347 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
348 +        case MAX:
349 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
350 +        default:
351 +          sprintf(painCave.errMsg,
352 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
353 +                  "hit an unknown cutoff policy!\n");
354 +          painCave.severity = OPENMD_ERROR;
355 +          painCave.isFatal = 1;
356 +          simError();              
357 +        }
358 +
359 +        pair<int,int> key = make_pair(i,j);
360 +        gTypeCutoffMap[key].first = thisRcut;
361 +
362 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363 +
364 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
365 +        
366 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367 +
368 +        // sanity check
369 +        
370 +        if (userChoseCutoff_) {
371 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
372 +            sprintf(painCave.errMsg,
373 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
374 +                    "user-specified rCut does not match computed group Cutoff\n");
375 +            painCave.severity = OPENMD_ERROR;
376 +            painCave.isFatal = 1;
377 +            simError();            
378 +          }
379 +        }
380 +      }
381 +    }
382 +  }
383 +
384 +
385 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
386 +    int i, j;
387 +
388 + #ifdef IS_MPI
389 +    i = groupRowToGtype[cg1];
390 +    j = groupColToGtype[cg2];
391 + #else
392 +    i = groupToGtype[cg1];
393 +    j = groupToGtype[cg2];
394 + #endif
395 +    
396 +    return gTypeCutoffMap[make_pair(i,j)];
397 +  }
398 +
399 +
400    void ForceMatrixDecomposition::zeroWorkArrays() {
401  
402      for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
# Line 765 | Line 934 | namespace OpenMD {
934    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
935        
936      vector<pair<int, int> > neighborList;
937 +    groupCutoffs cuts;
938   #ifdef IS_MPI
939      cellListRow_.clear();
940      cellListCol_.clear();
# Line 772 | Line 942 | namespace OpenMD {
942      cellList_.clear();
943   #endif
944  
945 <    // dangerous to not do error checking.
776 <    RealType rCut_;
777 <
778 <    RealType rList_ = (rCut_ + skinThickness_);
945 >    RealType rList_ = (largestRcut_ + skinThickness_);
946      RealType rl2 = rList_ * rList_;
947      Snapshot* snap_ = sman_->getCurrentSnapshot();
948      Mat3x3d Hmat = snap_->getHmat();
# Line 898 | Line 1065 | namespace OpenMD {
1065                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1066                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1067                    snap_->wrapVector(dr);
1068 <                  if (dr.lengthSquare() < rl2) {
1068 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1069 >                  if (dr.lengthSquare() < cuts.third) {
1070                      neighborList.push_back(make_pair((*j1), (*j2)));
1071                    }
1072                  }
# Line 917 | Line 1085 | namespace OpenMD {
1085                  if (m2 != m1 || (*j2) < (*j1)) {
1086                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1087                    snap_->wrapVector(dr);
1088 <                  if (dr.lengthSquare() < rl2) {
1088 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1089 >                  if (dr.lengthSquare() < cuts.third) {
1090                      neighborList.push_back(make_pair((*j1), (*j2)));
1091                    }
1092                  }

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