# | Line 42 | Line 42 | |
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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 { | |
# | Line 54 | Line 55 | namespace OpenMD { | |
55 | void ForceMatrixDecomposition::distributeInitialData() { | |
56 | snap_ = sman_->getCurrentSnapshot(); | |
57 | storageLayout_ = sman_->getStorageLayout(); | |
58 | < | #ifdef IS_MPI |
59 | < | int nLocal = snap_->getNumberOfAtoms(); |
59 | < | int nGroups = snap_->getNumberOfCutoffGroups(); |
58 | > | ff_ = info_->getForceField(); |
59 | > | nLocal_ = snap_->getNumberOfAtoms(); |
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); |
61 | > | nGroups_ = info_->getNLocalCutoffGroups(); |
62 | > | // gather the information for atomtype IDs (atids): |
63 | > | idents = info_->getIdentArray(); |
64 | > | AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
65 | > | cgLocalToGlobal = info_->getGlobalGroupIndices(); |
66 | > | vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); |
67 | ||
68 | < | 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); |
68 | > | massFactors = info_->getMassFactors(); |
69 | ||
70 | < | cgCommIntRow = new Communicator<Row,int>(nGroups); |
71 | < | cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups); |
72 | < | cgCommIntColumn = new Communicator<Column,int>(nGroups); |
73 | < | cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups); |
70 | > | PairList* excludes = info_->getExcludedInteractions(); |
71 | > | PairList* oneTwo = info_->getOneTwoInteractions(); |
72 | > | PairList* oneThree = info_->getOneThreeInteractions(); |
73 | > | PairList* oneFour = info_->getOneFourInteractions(); |
74 | ||
75 | < | int nAtomsInRow = AtomCommIntRow->getSize(); |
76 | < | int nAtomsInCol = AtomCommIntColumn->getSize(); |
77 | < | int nGroupsInRow = cgCommIntRow->getSize(); |
78 | < | int nGroupsInCol = cgCommIntColumn->getSize(); |
75 | > | #ifdef IS_MPI |
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 | + | 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 | + | nAtomsInRow_ = AtomCommIntRow->getSize(); |
95 | + | nAtomsInCol_ = AtomCommIntColumn->getSize(); |
96 | + | nGroupsInRow_ = cgCommIntRow->getSize(); |
97 | + | nGroupsInCol_ = cgCommIntColumn->getSize(); |
98 | + | |
99 | // Modify the data storage objects with the correct layouts and sizes: | |
100 | < | atomRowData.resize(nAtomsInRow); |
100 | > | atomRowData.resize(nAtomsInRow_); |
101 | atomRowData.setStorageLayout(storageLayout_); | |
102 | < | atomColData.resize(nAtomsInCol); |
102 | > | atomColData.resize(nAtomsInCol_); |
103 | atomColData.setStorageLayout(storageLayout_); | |
104 | < | cgRowData.resize(nGroupsInRow); |
104 | > | cgRowData.resize(nGroupsInRow_); |
105 | cgRowData.setStorageLayout(DataStorage::dslPosition); | |
106 | < | cgColData.resize(nGroupsInCol); |
106 | > | cgColData.resize(nGroupsInCol_); |
107 | cgColData.setStorageLayout(DataStorage::dslPosition); | |
108 | + | |
109 | + | identsRow.resize(nAtomsInRow_); |
110 | + | identsCol.resize(nAtomsInCol_); |
111 | ||
112 | < | vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
113 | < | vector<RealType> (nAtomsInRow, 0.0)); |
93 | < | vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
94 | < | vector<RealType> (nAtomsInCol, 0.0)); |
95 | < | |
96 | < | |
97 | < | vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
112 | > | AtomCommIntRow->gather(idents, identsRow); |
113 | > | AtomCommIntColumn->gather(idents, identsCol); |
114 | ||
115 | < | // gather the information for atomtype IDs (atids): |
116 | < | vector<int> identsLocal = info_->getIdentArray(); |
117 | < | identsRow.reserve(nAtomsInRow); |
118 | < | identsCol.reserve(nAtomsInCol); |
103 | < | |
104 | < | AtomCommIntRow->gather(identsLocal, identsRow); |
105 | < | AtomCommIntColumn->gather(identsLocal, identsCol); |
106 | < | |
107 | < | AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
115 | > | vector<int>::iterator it; |
116 | > | for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) { |
117 | > | cerr << "my AtomLocalToGlobal = " << (*it) << "\n"; |
118 | > | } |
119 | AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); | |
120 | AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); | |
121 | ||
111 | – | cgLocalToGlobal = info_->getGlobalGroupIndices(); |
122 | cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); | |
123 | cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); | |
124 | ||
125 | < | // still need: |
126 | < | // topoDist |
127 | < | // exclude |
125 | > | AtomCommRealRow->gather(massFactors, massFactorsRow); |
126 | > | AtomCommRealColumn->gather(massFactors, massFactorsCol); |
127 | > | |
128 | > | groupListRow_.clear(); |
129 | > | groupListRow_.resize(nGroupsInRow_); |
130 | > | for (int i = 0; i < nGroupsInRow_; i++) { |
131 | > | int gid = cgRowToGlobal[i]; |
132 | > | for (int j = 0; j < nAtomsInRow_; j++) { |
133 | > | int aid = AtomRowToGlobal[j]; |
134 | > | if (globalGroupMembership[aid] == gid) |
135 | > | groupListRow_[i].push_back(j); |
136 | > | } |
137 | > | } |
138 | > | |
139 | > | groupListCol_.clear(); |
140 | > | groupListCol_.resize(nGroupsInCol_); |
141 | > | for (int i = 0; i < nGroupsInCol_; i++) { |
142 | > | int gid = cgColToGlobal[i]; |
143 | > | for (int j = 0; j < nAtomsInCol_; j++) { |
144 | > | int aid = AtomColToGlobal[j]; |
145 | > | if (globalGroupMembership[aid] == gid) |
146 | > | groupListCol_[i].push_back(j); |
147 | > | } |
148 | > | } |
149 | > | |
150 | > | excludesForAtom.clear(); |
151 | > | excludesForAtom.resize(nAtomsInRow_); |
152 | > | toposForAtom.clear(); |
153 | > | toposForAtom.resize(nAtomsInRow_); |
154 | > | topoDist.clear(); |
155 | > | topoDist.resize(nAtomsInRow_); |
156 | > | for (int i = 0; i < nAtomsInRow_; i++) { |
157 | > | int iglob = AtomRowToGlobal[i]; |
158 | > | |
159 | > | for (int j = 0; j < nAtomsInCol_; j++) { |
160 | > | int jglob = AtomColToGlobal[j]; |
161 | > | |
162 | > | if (excludes->hasPair(iglob, jglob)) |
163 | > | excludesForAtom[i].push_back(j); |
164 | > | |
165 | > | if (oneTwo->hasPair(iglob, jglob)) { |
166 | > | toposForAtom[i].push_back(j); |
167 | > | topoDist[i].push_back(1); |
168 | > | } else { |
169 | > | if (oneThree->hasPair(iglob, jglob)) { |
170 | > | toposForAtom[i].push_back(j); |
171 | > | topoDist[i].push_back(2); |
172 | > | } else { |
173 | > | if (oneFour->hasPair(iglob, jglob)) { |
174 | > | toposForAtom[i].push_back(j); |
175 | > | topoDist[i].push_back(3); |
176 | > | } |
177 | > | } |
178 | > | } |
179 | > | } |
180 | > | } |
181 | > | |
182 | > | #endif |
183 | > | |
184 | > | groupList_.clear(); |
185 | > | groupList_.resize(nGroups_); |
186 | > | for (int i = 0; i < nGroups_; i++) { |
187 | > | int gid = cgLocalToGlobal[i]; |
188 | > | for (int j = 0; j < nLocal_; j++) { |
189 | > | int aid = AtomLocalToGlobal[j]; |
190 | > | if (globalGroupMembership[aid] == gid) { |
191 | > | groupList_[i].push_back(j); |
192 | > | } |
193 | > | } |
194 | > | } |
195 | > | |
196 | > | excludesForAtom.clear(); |
197 | > | excludesForAtom.resize(nLocal_); |
198 | > | toposForAtom.clear(); |
199 | > | toposForAtom.resize(nLocal_); |
200 | > | topoDist.clear(); |
201 | > | topoDist.resize(nLocal_); |
202 | > | |
203 | > | for (int i = 0; i < nLocal_; i++) { |
204 | > | int iglob = AtomLocalToGlobal[i]; |
205 | > | |
206 | > | for (int j = 0; j < nLocal_; j++) { |
207 | > | int jglob = AtomLocalToGlobal[j]; |
208 | > | |
209 | > | if (excludes->hasPair(iglob, jglob)) |
210 | > | excludesForAtom[i].push_back(j); |
211 | > | |
212 | > | if (oneTwo->hasPair(iglob, jglob)) { |
213 | > | toposForAtom[i].push_back(j); |
214 | > | topoDist[i].push_back(1); |
215 | > | } else { |
216 | > | if (oneThree->hasPair(iglob, jglob)) { |
217 | > | toposForAtom[i].push_back(j); |
218 | > | topoDist[i].push_back(2); |
219 | > | } else { |
220 | > | if (oneFour->hasPair(iglob, jglob)) { |
221 | > | toposForAtom[i].push_back(j); |
222 | > | topoDist[i].push_back(3); |
223 | > | } |
224 | > | } |
225 | > | } |
226 | > | } |
227 | > | } |
228 | > | |
229 | > | createGtypeCutoffMap(); |
230 | > | |
231 | > | } |
232 | > | |
233 | > | void ForceMatrixDecomposition::createGtypeCutoffMap() { |
234 | > | |
235 | > | RealType tol = 1e-6; |
236 | > | RealType rc; |
237 | > | int atid; |
238 | > | set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
239 | > | map<int, RealType> atypeCutoff; |
240 | > | |
241 | > | for (set<AtomType*>::iterator at = atypes.begin(); |
242 | > | at != atypes.end(); ++at){ |
243 | > | atid = (*at)->getIdent(); |
244 | > | if (userChoseCutoff_) |
245 | > | atypeCutoff[atid] = userCutoff_; |
246 | > | else |
247 | > | atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
248 | > | } |
249 | > | |
250 | > | vector<RealType> gTypeCutoffs; |
251 | > | // first we do a single loop over the cutoff groups to find the |
252 | > | // largest cutoff for any atypes present in this group. |
253 | > | #ifdef IS_MPI |
254 | > | vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0); |
255 | > | groupRowToGtype.resize(nGroupsInRow_); |
256 | > | for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) { |
257 | > | vector<int> atomListRow = getAtomsInGroupRow(cg1); |
258 | > | for (vector<int>::iterator ia = atomListRow.begin(); |
259 | > | ia != atomListRow.end(); ++ia) { |
260 | > | int atom1 = (*ia); |
261 | > | atid = identsRow[atom1]; |
262 | > | if (atypeCutoff[atid] > groupCutoffRow[cg1]) { |
263 | > | groupCutoffRow[cg1] = atypeCutoff[atid]; |
264 | > | } |
265 | > | } |
266 | > | |
267 | > | bool gTypeFound = false; |
268 | > | for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
269 | > | if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) { |
270 | > | groupRowToGtype[cg1] = gt; |
271 | > | gTypeFound = true; |
272 | > | } |
273 | > | } |
274 | > | if (!gTypeFound) { |
275 | > | gTypeCutoffs.push_back( groupCutoffRow[cg1] ); |
276 | > | groupRowToGtype[cg1] = gTypeCutoffs.size() - 1; |
277 | > | } |
278 | > | |
279 | > | } |
280 | > | vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0); |
281 | > | groupColToGtype.resize(nGroupsInCol_); |
282 | > | for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) { |
283 | > | vector<int> atomListCol = getAtomsInGroupColumn(cg2); |
284 | > | for (vector<int>::iterator jb = atomListCol.begin(); |
285 | > | jb != atomListCol.end(); ++jb) { |
286 | > | int atom2 = (*jb); |
287 | > | atid = identsCol[atom2]; |
288 | > | if (atypeCutoff[atid] > groupCutoffCol[cg2]) { |
289 | > | groupCutoffCol[cg2] = atypeCutoff[atid]; |
290 | > | } |
291 | > | } |
292 | > | bool gTypeFound = false; |
293 | > | for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
294 | > | if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) { |
295 | > | groupColToGtype[cg2] = gt; |
296 | > | gTypeFound = true; |
297 | > | } |
298 | > | } |
299 | > | if (!gTypeFound) { |
300 | > | gTypeCutoffs.push_back( groupCutoffCol[cg2] ); |
301 | > | groupColToGtype[cg2] = gTypeCutoffs.size() - 1; |
302 | > | } |
303 | > | } |
304 | > | #else |
305 | > | |
306 | > | vector<RealType> groupCutoff(nGroups_, 0.0); |
307 | > | groupToGtype.resize(nGroups_); |
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 | + | // Now we find the maximum group cutoff value present in the simulation |
337 | + | |
338 | + | RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
339 | + | |
340 | + | #ifdef IS_MPI |
341 | + | MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX); |
342 | + | #endif |
343 | + | |
344 | + | RealType tradRcut = groupMax; |
345 | + | |
346 | + | for (int i = 0; i < gTypeCutoffs.size(); i++) { |
347 | + | for (int j = 0; j < gTypeCutoffs.size(); j++) { |
348 | + | RealType thisRcut; |
349 | + | switch(cutoffPolicy_) { |
350 | + | case TRADITIONAL: |
351 | + | thisRcut = tradRcut; |
352 | + | break; |
353 | + | case MIX: |
354 | + | thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]); |
355 | + | break; |
356 | + | case MAX: |
357 | + | thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]); |
358 | + | break; |
359 | + | default: |
360 | + | sprintf(painCave.errMsg, |
361 | + | "ForceMatrixDecomposition::createGtypeCutoffMap " |
362 | + | "hit an unknown cutoff policy!\n"); |
363 | + | painCave.severity = OPENMD_ERROR; |
364 | + | painCave.isFatal = 1; |
365 | + | simError(); |
366 | + | break; |
367 | + | } |
368 | + | |
369 | + | pair<int,int> key = make_pair(i,j); |
370 | + | gTypeCutoffMap[key].first = thisRcut; |
371 | + | |
372 | + | if (thisRcut > largestRcut_) largestRcut_ = thisRcut; |
373 | + | |
374 | + | gTypeCutoffMap[key].second = thisRcut*thisRcut; |
375 | + | |
376 | + | gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); |
377 | + | |
378 | + | // sanity check |
379 | + | |
380 | + | if (userChoseCutoff_) { |
381 | + | if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) { |
382 | + | sprintf(painCave.errMsg, |
383 | + | "ForceMatrixDecomposition::createGtypeCutoffMap " |
384 | + | "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_); |
385 | + | painCave.severity = OPENMD_ERROR; |
386 | + | painCave.isFatal = 1; |
387 | + | simError(); |
388 | + | } |
389 | + | } |
390 | + | } |
391 | + | } |
392 | } | |
393 | + | |
394 | + | |
395 | + | groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) { |
396 | + | int i, j; |
397 | + | #ifdef IS_MPI |
398 | + | i = groupRowToGtype[cg1]; |
399 | + | j = groupColToGtype[cg2]; |
400 | + | #else |
401 | + | i = groupToGtype[cg1]; |
402 | + | j = groupToGtype[cg2]; |
403 | + | #endif |
404 | + | return gTypeCutoffMap[make_pair(i,j)]; |
405 | + | } |
406 | + | |
407 | + | int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) { |
408 | + | for (int j = 0; j < toposForAtom[atom1].size(); j++) { |
409 | + | if (toposForAtom[atom1][j] == atom2) |
410 | + | return topoDist[atom1][j]; |
411 | + | } |
412 | + | return 0; |
413 | + | } |
414 | + | |
415 | + | void ForceMatrixDecomposition::zeroWorkArrays() { |
416 | + | pairwisePot = 0.0; |
417 | + | embeddingPot = 0.0; |
418 | + | |
419 | + | #ifdef IS_MPI |
420 | + | if (storageLayout_ & DataStorage::dslForce) { |
421 | + | fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero); |
422 | + | fill(atomColData.force.begin(), atomColData.force.end(), V3Zero); |
423 | + | } |
424 | + | |
425 | + | if (storageLayout_ & DataStorage::dslTorque) { |
426 | + | fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero); |
427 | + | fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero); |
428 | + | } |
429 | ||
430 | + | fill(pot_row.begin(), pot_row.end(), |
431 | + | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
432 | ||
433 | + | fill(pot_col.begin(), pot_col.end(), |
434 | + | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
435 | ||
436 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
437 | + | fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0); |
438 | + | fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0); |
439 | + | } |
440 | + | |
441 | + | if (storageLayout_ & DataStorage::dslDensity) { |
442 | + | fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0); |
443 | + | fill(atomColData.density.begin(), atomColData.density.end(), 0.0); |
444 | + | } |
445 | + | |
446 | + | if (storageLayout_ & DataStorage::dslFunctional) { |
447 | + | fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0); |
448 | + | fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0); |
449 | + | } |
450 | + | |
451 | + | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
452 | + | fill(atomRowData.functionalDerivative.begin(), |
453 | + | atomRowData.functionalDerivative.end(), 0.0); |
454 | + | fill(atomColData.functionalDerivative.begin(), |
455 | + | atomColData.functionalDerivative.end(), 0.0); |
456 | + | } |
457 | + | |
458 | + | if (storageLayout_ & DataStorage::dslSkippedCharge) { |
459 | + | fill(atomRowData.skippedCharge.begin(), |
460 | + | atomRowData.skippedCharge.end(), 0.0); |
461 | + | fill(atomColData.skippedCharge.begin(), |
462 | + | atomColData.skippedCharge.end(), 0.0); |
463 | + | } |
464 | + | |
465 | + | #else |
466 | + | |
467 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
468 | + | fill(snap_->atomData.particlePot.begin(), |
469 | + | snap_->atomData.particlePot.end(), 0.0); |
470 | + | } |
471 | + | |
472 | + | if (storageLayout_ & DataStorage::dslDensity) { |
473 | + | fill(snap_->atomData.density.begin(), |
474 | + | snap_->atomData.density.end(), 0.0); |
475 | + | } |
476 | + | if (storageLayout_ & DataStorage::dslFunctional) { |
477 | + | fill(snap_->atomData.functional.begin(), |
478 | + | snap_->atomData.functional.end(), 0.0); |
479 | + | } |
480 | + | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
481 | + | fill(snap_->atomData.functionalDerivative.begin(), |
482 | + | snap_->atomData.functionalDerivative.end(), 0.0); |
483 | + | } |
484 | + | if (storageLayout_ & DataStorage::dslSkippedCharge) { |
485 | + | fill(snap_->atomData.skippedCharge.begin(), |
486 | + | snap_->atomData.skippedCharge.end(), 0.0); |
487 | + | } |
488 | + | #endif |
489 | + | |
490 | + | } |
491 | + | |
492 | + | |
493 | void ForceMatrixDecomposition::distributeData() { | |
494 | snap_ = sman_->getCurrentSnapshot(); | |
495 | storageLayout_ = sman_->getStorageLayout(); | |
# | Line 155 | Line 525 | namespace OpenMD { | |
525 | #endif | |
526 | } | |
527 | ||
528 | + | /* collects information obtained during the pre-pair loop onto local |
529 | + | * data structures. |
530 | + | */ |
531 | void ForceMatrixDecomposition::collectIntermediateData() { | |
532 | snap_ = sman_->getCurrentSnapshot(); | |
533 | storageLayout_ = sman_->getStorageLayout(); | |
# | Line 166 | Line 539 | namespace OpenMD { | |
539 | snap_->atomData.density); | |
540 | ||
541 | int n = snap_->atomData.density.size(); | |
542 | < | std::vector<RealType> rho_tmp(n, 0.0); |
542 | > | vector<RealType> rho_tmp(n, 0.0); |
543 | AtomCommRealColumn->scatter(atomColData.density, rho_tmp); | |
544 | for (int i = 0; i < n; i++) | |
545 | snap_->atomData.density[i] += rho_tmp[i]; | |
546 | } | |
547 | #endif | |
548 | } | |
549 | < | |
549 | > | |
550 | > | /* |
551 | > | * redistributes information obtained during the pre-pair loop out to |
552 | > | * row and column-indexed data structures |
553 | > | */ |
554 | void ForceMatrixDecomposition::distributeIntermediateData() { | |
555 | snap_ = sman_->getCurrentSnapshot(); | |
556 | storageLayout_ = sman_->getStorageLayout(); | |
# | Line 215 | Line 592 | namespace OpenMD { | |
592 | ||
593 | if (storageLayout_ & DataStorage::dslTorque) { | |
594 | ||
595 | < | int nt = snap_->atomData.force.size(); |
595 | > | int nt = snap_->atomData.torque.size(); |
596 | vector<Vector3d> trq_tmp(nt, V3Zero); | |
597 | ||
598 | AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); | |
599 | < | for (int i = 0; i < n; i++) { |
599 | > | for (int i = 0; i < nt; i++) { |
600 | snap_->atomData.torque[i] += trq_tmp[i]; | |
601 | trq_tmp[i] = 0.0; | |
602 | } | |
603 | ||
604 | AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); | |
605 | < | for (int i = 0; i < n; i++) |
605 | > | for (int i = 0; i < nt; i++) |
606 | snap_->atomData.torque[i] += trq_tmp[i]; | |
607 | } | |
231 | – | |
232 | – | int nLocal = snap_->getNumberOfAtoms(); |
608 | ||
609 | < | vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
610 | < | vector<RealType> (nLocal, 0.0)); |
611 | < | |
612 | < | for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
613 | < | AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
614 | < | for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
615 | < | pot_local[i] += pot_temp[i][ii]; |
609 | > | if (storageLayout_ & DataStorage::dslSkippedCharge) { |
610 | > | |
611 | > | int ns = snap_->atomData.skippedCharge.size(); |
612 | > | vector<RealType> skch_tmp(ns, 0.0); |
613 | > | |
614 | > | AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
615 | > | for (int i = 0; i < ns; i++) { |
616 | > | snap_->atomData.skippedCharge[i] = skch_tmp[i]; |
617 | > | skch_tmp[i] = 0.0; |
618 | } | |
619 | + | |
620 | + | AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
621 | + | for (int i = 0; i < ns; i++) |
622 | + | snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
623 | } | |
624 | + | |
625 | + | nLocal_ = snap_->getNumberOfAtoms(); |
626 | + | |
627 | + | vector<potVec> pot_temp(nLocal_, |
628 | + | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
629 | + | |
630 | + | // scatter/gather pot_row into the members of my column |
631 | + | |
632 | + | AtomCommPotRow->scatter(pot_row, pot_temp); |
633 | + | |
634 | + | for (int ii = 0; ii < pot_temp.size(); ii++ ) |
635 | + | pairwisePot += pot_temp[ii]; |
636 | + | |
637 | + | fill(pot_temp.begin(), pot_temp.end(), |
638 | + | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
639 | + | |
640 | + | AtomCommPotColumn->scatter(pot_col, pot_temp); |
641 | + | |
642 | + | for (int ii = 0; ii < pot_temp.size(); ii++ ) |
643 | + | pairwisePot += pot_temp[ii]; |
644 | #endif | |
645 | + | |
646 | } | |
647 | ||
648 | + | int ForceMatrixDecomposition::getNAtomsInRow() { |
649 | + | #ifdef IS_MPI |
650 | + | return nAtomsInRow_; |
651 | + | #else |
652 | + | return nLocal_; |
653 | + | #endif |
654 | + | } |
655 | + | |
656 | + | /** |
657 | + | * returns the list of atoms belonging to this group. |
658 | + | */ |
659 | + | vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){ |
660 | + | #ifdef IS_MPI |
661 | + | return groupListRow_[cg1]; |
662 | + | #else |
663 | + | return groupList_[cg1]; |
664 | + | #endif |
665 | + | } |
666 | + | |
667 | + | vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){ |
668 | + | #ifdef IS_MPI |
669 | + | return groupListCol_[cg2]; |
670 | + | #else |
671 | + | return groupList_[cg2]; |
672 | + | #endif |
673 | + | } |
674 | ||
675 | Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ | |
676 | Vector3d d; | |
# | Line 284 | Line 712 | namespace OpenMD { | |
712 | snap_->wrapVector(d); | |
713 | return d; | |
714 | } | |
715 | + | |
716 | + | RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) { |
717 | + | #ifdef IS_MPI |
718 | + | return massFactorsRow[atom1]; |
719 | + | #else |
720 | + | return massFactors[atom1]; |
721 | + | #endif |
722 | + | } |
723 | + | |
724 | + | RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) { |
725 | + | #ifdef IS_MPI |
726 | + | return massFactorsCol[atom2]; |
727 | + | #else |
728 | + | return massFactors[atom2]; |
729 | + | #endif |
730 | + | |
731 | + | } |
732 | ||
733 | Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ | |
734 | Vector3d d; | |
# | Line 298 | Line 743 | namespace OpenMD { | |
743 | return d; | |
744 | } | |
745 | ||
746 | + | vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) { |
747 | + | return excludesForAtom[atom1]; |
748 | + | } |
749 | + | |
750 | + | /** |
751 | + | * We need to exclude some overcounted interactions that result from |
752 | + | * the parallel decomposition. |
753 | + | */ |
754 | + | bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
755 | + | int unique_id_1, unique_id_2; |
756 | + | |
757 | + | #ifdef IS_MPI |
758 | + | // in MPI, we have to look up the unique IDs for each atom |
759 | + | unique_id_1 = AtomRowToGlobal[atom1]; |
760 | + | unique_id_2 = AtomColToGlobal[atom2]; |
761 | + | |
762 | + | // this situation should only arise in MPI simulations |
763 | + | if (unique_id_1 == unique_id_2) return true; |
764 | + | |
765 | + | // this prevents us from doing the pair on multiple processors |
766 | + | if (unique_id_1 < unique_id_2) { |
767 | + | if ((unique_id_1 + unique_id_2) % 2 == 0) return true; |
768 | + | } else { |
769 | + | if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
770 | + | } |
771 | + | #endif |
772 | + | return false; |
773 | + | } |
774 | + | |
775 | + | /** |
776 | + | * We need to handle the interactions for atoms who are involved in |
777 | + | * the same rigid body as well as some short range interactions |
778 | + | * (bonds, bends, torsions) differently from other interactions. |
779 | + | * We'll still visit the pairwise routines, but with a flag that |
780 | + | * tells those routines to exclude the pair from direct long range |
781 | + | * interactions. Some indirect interactions (notably reaction |
782 | + | * field) must still be handled for these pairs. |
783 | + | */ |
784 | + | bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
785 | + | int unique_id_2; |
786 | + | |
787 | + | #ifdef IS_MPI |
788 | + | // in MPI, we have to look up the unique IDs for the row atom. |
789 | + | unique_id_2 = AtomColToGlobal[atom2]; |
790 | + | #else |
791 | + | // in the normal loop, the atom numbers are unique |
792 | + | unique_id_2 = atom2; |
793 | + | #endif |
794 | + | |
795 | + | for (vector<int>::iterator i = excludesForAtom[atom1].begin(); |
796 | + | i != excludesForAtom[atom1].end(); ++i) { |
797 | + | if ( (*i) == unique_id_2 ) return true; |
798 | + | } |
799 | + | |
800 | + | return false; |
801 | + | } |
802 | + | |
803 | + | |
804 | void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ | |
805 | #ifdef IS_MPI | |
806 | atomRowData.force[atom1] += fg; | |
# | Line 312 | Line 815 | namespace OpenMD { | |
815 | #else | |
816 | snap_->atomData.force[atom2] += fg; | |
817 | #endif | |
315 | – | |
818 | } | |
819 | ||
820 | // filling interaction blocks with pointers | |
821 | < | InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
821 | > | void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, |
822 | > | int atom1, int atom2) { |
823 | ||
824 | < | InteractionData idat; |
824 | > | idat.excluded = excludeAtomPair(atom1, atom2); |
825 | > | |
826 | #ifdef IS_MPI | |
827 | + | |
828 | + | idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
829 | + | ff_->getAtomType(identsCol[atom2]) ); |
830 | + | |
831 | if (storageLayout_ & DataStorage::dslAmat) { | |
832 | idat.A1 = &(atomRowData.aMat[atom1]); | |
833 | idat.A2 = &(atomColData.aMat[atom2]); | |
834 | } | |
835 | < | |
835 | > | |
836 | if (storageLayout_ & DataStorage::dslElectroFrame) { | |
837 | idat.eFrame1 = &(atomRowData.electroFrame[atom1]); | |
838 | idat.eFrame2 = &(atomColData.electroFrame[atom2]); | |
# | Line 340 | Line 848 | namespace OpenMD { | |
848 | idat.rho2 = &(atomColData.density[atom2]); | |
849 | } | |
850 | ||
851 | + | if (storageLayout_ & DataStorage::dslFunctional) { |
852 | + | idat.frho1 = &(atomRowData.functional[atom1]); |
853 | + | idat.frho2 = &(atomColData.functional[atom2]); |
854 | + | } |
855 | + | |
856 | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { | |
857 | idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); | |
858 | idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); | |
859 | } | |
860 | + | |
861 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
862 | + | idat.particlePot1 = &(atomRowData.particlePot[atom1]); |
863 | + | idat.particlePot2 = &(atomColData.particlePot[atom2]); |
864 | + | } |
865 | + | |
866 | + | if (storageLayout_ & DataStorage::dslSkippedCharge) { |
867 | + | idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
868 | + | idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
869 | + | } |
870 | + | |
871 | #else | |
872 | + | |
873 | + | idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
874 | + | ff_->getAtomType(idents[atom2]) ); |
875 | + | |
876 | if (storageLayout_ & DataStorage::dslAmat) { | |
877 | idat.A1 = &(snap_->atomData.aMat[atom1]); | |
878 | idat.A2 = &(snap_->atomData.aMat[atom2]); | |
# | Line 360 | Line 888 | namespace OpenMD { | |
888 | idat.t2 = &(snap_->atomData.torque[atom2]); | |
889 | } | |
890 | ||
891 | < | if (storageLayout_ & DataStorage::dslDensity) { |
891 | > | if (storageLayout_ & DataStorage::dslDensity) { |
892 | idat.rho1 = &(snap_->atomData.density[atom1]); | |
893 | idat.rho2 = &(snap_->atomData.density[atom2]); | |
894 | } | |
895 | ||
896 | + | if (storageLayout_ & DataStorage::dslFunctional) { |
897 | + | idat.frho1 = &(snap_->atomData.functional[atom1]); |
898 | + | idat.frho2 = &(snap_->atomData.functional[atom2]); |
899 | + | } |
900 | + | |
901 | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { | |
902 | idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); | |
903 | idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); | |
904 | } | |
905 | + | |
906 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
907 | + | idat.particlePot1 = &(snap_->atomData.particlePot[atom1]); |
908 | + | idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
909 | + | } |
910 | + | |
911 | + | if (storageLayout_ & DataStorage::dslSkippedCharge) { |
912 | + | idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
913 | + | idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
914 | + | } |
915 | #endif | |
373 | – | |
916 | } | |
917 | < | InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
918 | < | InteractionData idat; |
919 | < | skippedCharge1 |
378 | < | skippedCharge2 |
379 | < | rij |
380 | < | d |
381 | < | electroMult |
382 | < | sw |
383 | < | f |
917 | > | |
918 | > | |
919 | > | void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
920 | #ifdef IS_MPI | |
921 | + | pot_row[atom1] += 0.5 * *(idat.pot); |
922 | + | pot_col[atom2] += 0.5 * *(idat.pot); |
923 | ||
924 | < | if (storageLayout_ & DataStorage::dslElectroFrame) { |
925 | < | idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
926 | < | idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
927 | < | } |
390 | < | if (storageLayout_ & DataStorage::dslTorque) { |
391 | < | idat.t1 = &(atomRowData.torque[atom1]); |
392 | < | idat.t2 = &(atomColData.torque[atom2]); |
393 | < | } |
924 | > | atomRowData.force[atom1] += *(idat.f1); |
925 | > | atomColData.force[atom2] -= *(idat.f1); |
926 | > | #else |
927 | > | pairwisePot += *(idat.pot); |
928 | ||
929 | + | snap_->atomData.force[atom1] += *(idat.f1); |
930 | + | snap_->atomData.force[atom2] -= *(idat.f1); |
931 | + | #endif |
932 | ||
933 | } | |
397 | – | SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
398 | – | } |
934 | ||
400 | – | |
935 | /* | |
936 | * buildNeighborList | |
937 | * | |
938 | * first element of pair is row-indexed CutoffGroup | |
939 | * second element of pair is column-indexed CutoffGroup | |
940 | */ | |
941 | < | vector<pair<int, int> > buildNeighborList() { |
942 | < | Vector3d dr, invWid, rs, shift; |
943 | < | Vector3i cc, m1v, m2s; |
944 | < | RealType rrNebr; |
945 | < | int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset; |
941 | > | vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
942 | > | |
943 | > | vector<pair<int, int> > neighborList; |
944 | > | groupCutoffs cuts; |
945 | > | bool doAllPairs = false; |
946 | ||
947 | + | #ifdef IS_MPI |
948 | + | cellListRow_.clear(); |
949 | + | cellListCol_.clear(); |
950 | + | #else |
951 | + | cellList_.clear(); |
952 | + | #endif |
953 | ||
954 | < | vector<pair<int, int> > neighborList; |
955 | < | Vector3i nCells; |
956 | < | Vector3d invWid, r; |
417 | < | |
418 | < | rList_ = (rCut_ + skinThickness_); |
419 | < | rl2 = rList_ * rList_; |
420 | < | |
421 | < | snap_ = sman_->getCurrentSnapshot(); |
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_; |
962 | > | nCells_.x() = (int) ( Hx.length() )/ rList_; |
963 | > | nCells_.y() = (int) ( Hy.length() )/ rList_; |
964 | > | nCells_.z() = (int) ( Hz.length() )/ rList_; |
965 | ||
966 | < | for (i = 0; i < nGroupsInRow; i++) { |
432 | < | rs = cgRowData.position[i]; |
433 | < | snap_->scaleVector(rs); |
434 | < | } |
966 | > | // handle small boxes where the cell offsets can end up repeating cells |
967 | ||
968 | + | if (nCells_.x() < 3) doAllPairs = true; |
969 | + | if (nCells_.y() < 3) doAllPairs = true; |
970 | + | if (nCells_.z() < 3) doAllPairs = true; |
971 | ||
972 | < | VDiv (invWid, cells, region); |
973 | < | for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1; |
974 | < | for (n = 0; n < nMol; n ++) { |
975 | < | VSAdd (rs, mol[n].r, 0.5, region); |
976 | < | 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(); |
972 | > | Mat3x3d invHmat = snap_->getInvHmat(); |
973 | > | Vector3d rs, scaled, dr; |
974 | > | Vector3i whichCell; |
975 | > | int cellIndex; |
976 | > | int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
977 | ||
978 | < | if (m2v.x() >= cells.x) { |
979 | < | m2v.x() = 0; |
980 | < | shift.x() = region.x(); |
981 | < | } else if (m2v.x() < 0) { |
982 | < | m2v.x() = cells.x() - 1; |
983 | < | shift.x() = - region.x(); |
462 | < | } |
978 | > | #ifdef IS_MPI |
979 | > | cellListRow_.resize(nCtot); |
980 | > | cellListCol_.resize(nCtot); |
981 | > | #else |
982 | > | cellList_.resize(nCtot); |
983 | > | #endif |
984 | ||
985 | < | if (m2v.y() >= cells.y()) { |
986 | < | 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 | < | } |
985 | > | if (!doAllPairs) { |
986 | > | #ifdef IS_MPI |
987 | ||
988 | < | m2 = VLinear (m2v, cells) + nMol; |
989 | < | for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) { |
990 | < | for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) { |
991 | < | if (m1 != m2 || j2 < j1) { |
992 | < | dr = mol[j1].r - mol[j2].r; |
993 | < | VSub (dr, mol[j1].r, mol[j2].r); |
994 | < | VVSub (dr, shift); |
995 | < | if (VLenSq (dr) < rrNebr) { |
996 | < | neighborList.push_back(make_pair(j1, j2)); |
988 | > | for (int i = 0; i < nGroupsInRow_; i++) { |
989 | > | rs = cgRowData.position[i]; |
990 | > | |
991 | > | // scaled positions relative to the box vectors |
992 | > | scaled = invHmat * rs; |
993 | > | |
994 | > | // wrap the vector back into the unit box by subtracting integer box |
995 | > | // numbers |
996 | > | for (int j = 0; j < 3; j++) { |
997 | > | scaled[j] -= roundMe(scaled[j]); |
998 | > | scaled[j] += 0.5; |
999 | > | } |
1000 | > | |
1001 | > | // find xyz-indices of cell that cutoffGroup is in. |
1002 | > | whichCell.x() = nCells_.x() * scaled.x(); |
1003 | > | whichCell.y() = nCells_.y() * scaled.y(); |
1004 | > | whichCell.z() = nCells_.z() * scaled.z(); |
1005 | > | |
1006 | > | // find single index of this cell: |
1007 | > | cellIndex = Vlinear(whichCell, nCells_); |
1008 | > | |
1009 | > | // add this cutoff group to the list of groups in this cell; |
1010 | > | cellListRow_[cellIndex].push_back(i); |
1011 | > | } |
1012 | > | |
1013 | > | for (int i = 0; i < nGroupsInCol_; i++) { |
1014 | > | rs = cgColData.position[i]; |
1015 | > | |
1016 | > | // scaled positions relative to the box vectors |
1017 | > | scaled = invHmat * rs; |
1018 | > | |
1019 | > | // wrap the vector back into the unit box by subtracting integer box |
1020 | > | // numbers |
1021 | > | for (int j = 0; j < 3; j++) { |
1022 | > | scaled[j] -= roundMe(scaled[j]); |
1023 | > | scaled[j] += 0.5; |
1024 | > | } |
1025 | > | |
1026 | > | // find xyz-indices of cell that cutoffGroup is in. |
1027 | > | whichCell.x() = nCells_.x() * scaled.x(); |
1028 | > | whichCell.y() = nCells_.y() * scaled.y(); |
1029 | > | whichCell.z() = nCells_.z() * scaled.z(); |
1030 | > | |
1031 | > | // find single index of this cell: |
1032 | > | cellIndex = Vlinear(whichCell, nCells_); |
1033 | > | |
1034 | > | // add this cutoff group to the list of groups in this cell; |
1035 | > | cellListCol_[cellIndex].push_back(i); |
1036 | > | } |
1037 | > | #else |
1038 | > | for (int i = 0; i < nGroups_; i++) { |
1039 | > | rs = snap_->cgData.position[i]; |
1040 | > | |
1041 | > | // scaled positions relative to the box vectors |
1042 | > | scaled = invHmat * rs; |
1043 | > | |
1044 | > | // wrap the vector back into the unit box by subtracting integer box |
1045 | > | // numbers |
1046 | > | for (int j = 0; j < 3; j++) { |
1047 | > | scaled[j] -= roundMe(scaled[j]); |
1048 | > | scaled[j] += 0.5; |
1049 | > | } |
1050 | > | |
1051 | > | // find xyz-indices of cell that cutoffGroup is in. |
1052 | > | whichCell.x() = nCells_.x() * scaled.x(); |
1053 | > | whichCell.y() = nCells_.y() * scaled.y(); |
1054 | > | whichCell.z() = nCells_.z() * scaled.z(); |
1055 | > | |
1056 | > | // find single index of this cell: |
1057 | > | cellIndex = Vlinear(whichCell, nCells_); |
1058 | > | |
1059 | > | // add this cutoff group to the list of groups in this cell; |
1060 | > | cellList_[cellIndex].push_back(i); |
1061 | > | } |
1062 | > | #endif |
1063 | > | |
1064 | > | for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
1065 | > | for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
1066 | > | for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
1067 | > | Vector3i m1v(m1x, m1y, m1z); |
1068 | > | int m1 = Vlinear(m1v, nCells_); |
1069 | > | |
1070 | > | for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
1071 | > | os != cellOffsets_.end(); ++os) { |
1072 | > | |
1073 | > | Vector3i m2v = m1v + (*os); |
1074 | > | |
1075 | > | if (m2v.x() >= nCells_.x()) { |
1076 | > | m2v.x() = 0; |
1077 | > | } else if (m2v.x() < 0) { |
1078 | > | m2v.x() = nCells_.x() - 1; |
1079 | > | } |
1080 | > | |
1081 | > | if (m2v.y() >= nCells_.y()) { |
1082 | > | m2v.y() = 0; |
1083 | > | } else if (m2v.y() < 0) { |
1084 | > | m2v.y() = nCells_.y() - 1; |
1085 | > | } |
1086 | > | |
1087 | > | if (m2v.z() >= nCells_.z()) { |
1088 | > | m2v.z() = 0; |
1089 | > | } else if (m2v.z() < 0) { |
1090 | > | m2v.z() = nCells_.z() - 1; |
1091 | > | } |
1092 | > | |
1093 | > | int m2 = Vlinear (m2v, nCells_); |
1094 | > | |
1095 | > | #ifdef IS_MPI |
1096 | > | for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
1097 | > | j1 != cellListRow_[m1].end(); ++j1) { |
1098 | > | for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
1099 | > | j2 != cellListCol_[m2].end(); ++j2) { |
1100 | > | |
1101 | > | // Always do this if we're in different cells or if |
1102 | > | // we're in the same cell and the global index of the |
1103 | > | // j2 cutoff group is less than the j1 cutoff group |
1104 | > | |
1105 | > | if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
1106 | > | dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
1107 | > | snap_->wrapVector(dr); |
1108 | > | cuts = getGroupCutoffs( (*j1), (*j2) ); |
1109 | > | if (dr.lengthSquare() < cuts.third) { |
1110 | > | neighborList.push_back(make_pair((*j1), (*j2))); |
1111 | > | } |
1112 | } | |
1113 | } | |
1114 | } | |
1115 | + | #else |
1116 | + | |
1117 | + | for (vector<int>::iterator j1 = cellList_[m1].begin(); |
1118 | + | j1 != cellList_[m1].end(); ++j1) { |
1119 | + | for (vector<int>::iterator j2 = cellList_[m2].begin(); |
1120 | + | j2 != cellList_[m2].end(); ++j2) { |
1121 | + | |
1122 | + | // Always do this if we're in different cells or if |
1123 | + | // we're in the same cell and the global index of the |
1124 | + | // j2 cutoff group is less than the j1 cutoff group |
1125 | + | |
1126 | + | if (m2 != m1 || (*j2) < (*j1)) { |
1127 | + | dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
1128 | + | snap_->wrapVector(dr); |
1129 | + | cuts = getGroupCutoffs( (*j1), (*j2) ); |
1130 | + | if (dr.lengthSquare() < cuts.third) { |
1131 | + | neighborList.push_back(make_pair((*j1), (*j2))); |
1132 | + | } |
1133 | + | } |
1134 | + | } |
1135 | + | } |
1136 | + | #endif |
1137 | } | |
1138 | } | |
1139 | } | |
1140 | } | |
1141 | + | } else { |
1142 | + | // branch to do all cutoff group pairs |
1143 | + | #ifdef IS_MPI |
1144 | + | for (int j1 = 0; j1 < nGroupsInRow_; j1++) { |
1145 | + | for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
1146 | + | dr = cgColData.position[j2] - cgRowData.position[j1]; |
1147 | + | snap_->wrapVector(dr); |
1148 | + | cuts = getGroupCutoffs( j1, j2 ); |
1149 | + | if (dr.lengthSquare() < cuts.third) { |
1150 | + | neighborList.push_back(make_pair(j1, j2)); |
1151 | + | } |
1152 | + | } |
1153 | + | } |
1154 | + | #else |
1155 | + | for (int j1 = 0; j1 < nGroups_ - 1; j1++) { |
1156 | + | for (int j2 = j1 + 1; j2 < nGroups_; j2++) { |
1157 | + | dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; |
1158 | + | snap_->wrapVector(dr); |
1159 | + | cuts = getGroupCutoffs( j1, j2 ); |
1160 | + | if (dr.lengthSquare() < cuts.third) { |
1161 | + | neighborList.push_back(make_pair(j1, j2)); |
1162 | + | } |
1163 | + | } |
1164 | + | } |
1165 | + | #endif |
1166 | } | |
1167 | + | |
1168 | + | // save the local cutoff group positions for the check that is |
1169 | + | // done on each loop: |
1170 | + | saved_CG_positions_.clear(); |
1171 | + | for (int i = 0; i < nGroups_; i++) |
1172 | + | saved_CG_positions_.push_back(snap_->cgData.position[i]); |
1173 | + | |
1174 | + | return neighborList; |
1175 | } | |
490 | – | |
491 | – | |
1176 | } //end namespace OpenMD |
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