# | Line 36 | Line 36 | |
---|---|---|
36 | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | |
37 | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | |
38 | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | |
39 | < | * [4] Vardeman & Gezelter, in progress (2009). |
39 | > | * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 | > | * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 | */ | |
42 | #include "parallel/ForceMatrixDecomposition.hpp" | |
43 | #include "math/SquareMatrix3.hpp" | |
# | Line 47 | Line 48 | namespace OpenMD { | |
48 | using namespace std; | |
49 | namespace OpenMD { | |
50 | ||
51 | + | ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) { |
52 | + | |
53 | + | // In a parallel computation, row and colum scans must visit all |
54 | + | // surrounding cells (not just the 14 upper triangular blocks that |
55 | + | // are used when the processor can see all pairs) |
56 | + | #ifdef IS_MPI |
57 | + | cellOffsets_.clear(); |
58 | + | cellOffsets_.push_back( Vector3i(-1,-1,-1) ); |
59 | + | cellOffsets_.push_back( Vector3i( 0,-1,-1) ); |
60 | + | cellOffsets_.push_back( Vector3i( 1,-1,-1) ); |
61 | + | cellOffsets_.push_back( Vector3i(-1, 0,-1) ); |
62 | + | cellOffsets_.push_back( Vector3i( 0, 0,-1) ); |
63 | + | cellOffsets_.push_back( Vector3i( 1, 0,-1) ); |
64 | + | cellOffsets_.push_back( Vector3i(-1, 1,-1) ); |
65 | + | cellOffsets_.push_back( Vector3i( 0, 1,-1) ); |
66 | + | cellOffsets_.push_back( Vector3i( 1, 1,-1) ); |
67 | + | cellOffsets_.push_back( Vector3i(-1,-1, 0) ); |
68 | + | cellOffsets_.push_back( Vector3i( 0,-1, 0) ); |
69 | + | cellOffsets_.push_back( Vector3i( 1,-1, 0) ); |
70 | + | cellOffsets_.push_back( Vector3i(-1, 0, 0) ); |
71 | + | cellOffsets_.push_back( Vector3i( 0, 0, 0) ); |
72 | + | cellOffsets_.push_back( Vector3i( 1, 0, 0) ); |
73 | + | cellOffsets_.push_back( Vector3i(-1, 1, 0) ); |
74 | + | cellOffsets_.push_back( Vector3i( 0, 1, 0) ); |
75 | + | cellOffsets_.push_back( Vector3i( 1, 1, 0) ); |
76 | + | cellOffsets_.push_back( Vector3i(-1,-1, 1) ); |
77 | + | cellOffsets_.push_back( Vector3i( 0,-1, 1) ); |
78 | + | cellOffsets_.push_back( Vector3i( 1,-1, 1) ); |
79 | + | cellOffsets_.push_back( Vector3i(-1, 0, 1) ); |
80 | + | cellOffsets_.push_back( Vector3i( 0, 0, 1) ); |
81 | + | cellOffsets_.push_back( Vector3i( 1, 0, 1) ); |
82 | + | cellOffsets_.push_back( Vector3i(-1, 1, 1) ); |
83 | + | cellOffsets_.push_back( Vector3i( 0, 1, 1) ); |
84 | + | cellOffsets_.push_back( Vector3i( 1, 1, 1) ); |
85 | + | #endif |
86 | + | } |
87 | + | |
88 | + | |
89 | /** | |
90 | * distributeInitialData is essentially a copy of the older fortran | |
91 | * SimulationSetup | |
92 | */ | |
54 | – | |
93 | void ForceMatrixDecomposition::distributeInitialData() { | |
94 | snap_ = sman_->getCurrentSnapshot(); | |
95 | storageLayout_ = sman_->getStorageLayout(); | |
96 | ff_ = info_->getForceField(); | |
97 | nLocal_ = snap_->getNumberOfAtoms(); | |
98 | < | |
98 | > | |
99 | nGroups_ = info_->getNLocalCutoffGroups(); | |
100 | // gather the information for atomtype IDs (atids): | |
101 | idents = info_->getIdentArray(); | |
# | Line 71 | Line 109 | namespace OpenMD { | |
109 | PairList* oneTwo = info_->getOneTwoInteractions(); | |
110 | PairList* oneThree = info_->getOneThreeInteractions(); | |
111 | PairList* oneFour = info_->getOneFourInteractions(); | |
112 | < | |
112 | > | |
113 | > | if (needVelocities_) |
114 | > | snap_->cgData.setStorageLayout(DataStorage::dslPosition | |
115 | > | DataStorage::dslVelocity); |
116 | > | else |
117 | > | snap_->cgData.setStorageLayout(DataStorage::dslPosition); |
118 | > | |
119 | #ifdef IS_MPI | |
120 | ||
121 | < | AtomCommIntRow = new Communicator<Row,int>(nLocal_); |
122 | < | 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_); |
121 | > | MPI::Intracomm row = rowComm.getComm(); |
122 | > | MPI::Intracomm col = colComm.getComm(); |
123 | ||
124 | < | AtomCommIntColumn = new Communicator<Column,int>(nLocal_); |
125 | < | AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_); |
126 | < | AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_); |
127 | < | AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_); |
128 | < | AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_); |
124 | > | AtomPlanIntRow = new Plan<int>(row, nLocal_); |
125 | > | AtomPlanRealRow = new Plan<RealType>(row, nLocal_); |
126 | > | AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_); |
127 | > | AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_); |
128 | > | AtomPlanPotRow = new Plan<potVec>(row, nLocal_); |
129 | ||
130 | < | cgCommIntRow = new Communicator<Row,int>(nGroups_); |
131 | < | cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_); |
132 | < | cgCommIntColumn = new Communicator<Column,int>(nGroups_); |
133 | < | cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_); |
130 | > | AtomPlanIntColumn = new Plan<int>(col, nLocal_); |
131 | > | AtomPlanRealColumn = new Plan<RealType>(col, nLocal_); |
132 | > | AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_); |
133 | > | AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_); |
134 | > | AtomPlanPotColumn = new Plan<potVec>(col, nLocal_); |
135 | ||
136 | < | nAtomsInRow_ = AtomCommIntRow->getSize(); |
137 | < | nAtomsInCol_ = AtomCommIntColumn->getSize(); |
138 | < | nGroupsInRow_ = cgCommIntRow->getSize(); |
139 | < | nGroupsInCol_ = cgCommIntColumn->getSize(); |
136 | > | cgPlanIntRow = new Plan<int>(row, nGroups_); |
137 | > | cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_); |
138 | > | cgPlanIntColumn = new Plan<int>(col, nGroups_); |
139 | > | cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_); |
140 | ||
141 | + | nAtomsInRow_ = AtomPlanIntRow->getSize(); |
142 | + | nAtomsInCol_ = AtomPlanIntColumn->getSize(); |
143 | + | nGroupsInRow_ = cgPlanIntRow->getSize(); |
144 | + | nGroupsInCol_ = cgPlanIntColumn->getSize(); |
145 | + | |
146 | // Modify the data storage objects with the correct layouts and sizes: | |
147 | atomRowData.resize(nAtomsInRow_); | |
148 | atomRowData.setStorageLayout(storageLayout_); | |
# | Line 104 | Line 151 | namespace OpenMD { | |
151 | cgRowData.resize(nGroupsInRow_); | |
152 | cgRowData.setStorageLayout(DataStorage::dslPosition); | |
153 | cgColData.resize(nGroupsInCol_); | |
154 | < | cgColData.setStorageLayout(DataStorage::dslPosition); |
155 | < | |
154 | > | if (needVelocities_) |
155 | > | // we only need column velocities if we need them. |
156 | > | cgColData.setStorageLayout(DataStorage::dslPosition | |
157 | > | DataStorage::dslVelocity); |
158 | > | else |
159 | > | cgColData.setStorageLayout(DataStorage::dslPosition); |
160 | > | |
161 | identsRow.resize(nAtomsInRow_); | |
162 | identsCol.resize(nAtomsInCol_); | |
163 | ||
164 | < | AtomCommIntRow->gather(idents, identsRow); |
165 | < | AtomCommIntColumn->gather(idents, identsCol); |
164 | > | AtomPlanIntRow->gather(idents, identsRow); |
165 | > | AtomPlanIntColumn->gather(idents, identsCol); |
166 | ||
167 | // allocate memory for the parallel objects | |
168 | + | atypesRow.resize(nAtomsInRow_); |
169 | + | atypesCol.resize(nAtomsInCol_); |
170 | + | |
171 | + | for (int i = 0; i < nAtomsInRow_; i++) |
172 | + | atypesRow[i] = ff_->getAtomType(identsRow[i]); |
173 | + | for (int i = 0; i < nAtomsInCol_; i++) |
174 | + | atypesCol[i] = ff_->getAtomType(identsCol[i]); |
175 | + | |
176 | + | pot_row.resize(nAtomsInRow_); |
177 | + | pot_col.resize(nAtomsInCol_); |
178 | + | |
179 | AtomRowToGlobal.resize(nAtomsInRow_); | |
180 | AtomColToGlobal.resize(nAtomsInCol_); | |
181 | + | AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
182 | + | AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
183 | + | |
184 | cgRowToGlobal.resize(nGroupsInRow_); | |
185 | cgColToGlobal.resize(nGroupsInCol_); | |
186 | + | cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
187 | + | cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
188 | + | |
189 | massFactorsRow.resize(nAtomsInRow_); | |
190 | massFactorsCol.resize(nAtomsInCol_); | |
191 | < | pot_row.resize(nAtomsInRow_); |
192 | < | pot_col.resize(nAtomsInCol_); |
191 | > | AtomPlanRealRow->gather(massFactors, massFactorsRow); |
192 | > | AtomPlanRealColumn->gather(massFactors, massFactorsCol); |
193 | ||
125 | – | AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
126 | – | AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
127 | – | |
128 | – | cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
129 | – | cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
130 | – | |
131 | – | AtomCommRealRow->gather(massFactors, massFactorsRow); |
132 | – | AtomCommRealColumn->gather(massFactors, massFactorsCol); |
133 | – | |
194 | groupListRow_.clear(); | |
195 | groupListRow_.resize(nGroupsInRow_); | |
196 | for (int i = 0; i < nGroupsInRow_; i++) { | |
# | Line 185 | Line 245 | namespace OpenMD { | |
245 | } | |
246 | } | |
247 | ||
248 | < | #endif |
189 | < | |
190 | < | groupList_.clear(); |
191 | < | groupList_.resize(nGroups_); |
192 | < | for (int i = 0; i < nGroups_; i++) { |
193 | < | int gid = cgLocalToGlobal[i]; |
194 | < | for (int j = 0; j < nLocal_; j++) { |
195 | < | int aid = AtomLocalToGlobal[j]; |
196 | < | if (globalGroupMembership[aid] == gid) { |
197 | < | groupList_[i].push_back(j); |
198 | < | } |
199 | < | } |
200 | < | } |
201 | < | |
248 | > | #else |
249 | excludesForAtom.clear(); | |
250 | excludesForAtom.resize(nLocal_); | |
251 | toposForAtom.clear(); | |
# | Line 231 | Line 278 | namespace OpenMD { | |
278 | } | |
279 | } | |
280 | } | |
281 | < | |
281 | > | #endif |
282 | > | |
283 | > | // allocate memory for the parallel objects |
284 | > | atypesLocal.resize(nLocal_); |
285 | > | |
286 | > | for (int i = 0; i < nLocal_; i++) |
287 | > | atypesLocal[i] = ff_->getAtomType(idents[i]); |
288 | > | |
289 | > | groupList_.clear(); |
290 | > | groupList_.resize(nGroups_); |
291 | > | for (int i = 0; i < nGroups_; i++) { |
292 | > | int gid = cgLocalToGlobal[i]; |
293 | > | for (int j = 0; j < nLocal_; j++) { |
294 | > | int aid = AtomLocalToGlobal[j]; |
295 | > | if (globalGroupMembership[aid] == gid) { |
296 | > | groupList_[i].push_back(j); |
297 | > | } |
298 | > | } |
299 | > | } |
300 | > | |
301 | > | |
302 | createGtypeCutoffMap(); | |
303 | ||
304 | } | |
# | Line 239 | Line 306 | namespace OpenMD { | |
306 | void ForceMatrixDecomposition::createGtypeCutoffMap() { | |
307 | ||
308 | RealType tol = 1e-6; | |
309 | + | largestRcut_ = 0.0; |
310 | RealType rc; | |
311 | int atid; | |
312 | set<AtomType*> atypes = info_->getSimulatedAtomTypes(); | |
313 | + | |
314 | map<int, RealType> atypeCutoff; | |
315 | ||
316 | for (set<AtomType*>::iterator at = atypes.begin(); | |
# | Line 249 | Line 318 | namespace OpenMD { | |
318 | atid = (*at)->getIdent(); | |
319 | if (userChoseCutoff_) | |
320 | atypeCutoff[atid] = userCutoff_; | |
321 | < | else |
321 | > | else |
322 | atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); | |
323 | } | |
324 | < | |
324 | > | |
325 | vector<RealType> gTypeCutoffs; | |
326 | // first we do a single loop over the cutoff groups to find the | |
327 | // largest cutoff for any atypes present in this group. | |
# | Line 312 | Line 381 | namespace OpenMD { | |
381 | vector<RealType> groupCutoff(nGroups_, 0.0); | |
382 | groupToGtype.resize(nGroups_); | |
383 | for (int cg1 = 0; cg1 < nGroups_; cg1++) { | |
315 | – | |
384 | groupCutoff[cg1] = 0.0; | |
385 | vector<int> atomList = getAtomsInGroupRow(cg1); | |
318 | – | |
386 | for (vector<int>::iterator ia = atomList.begin(); | |
387 | ia != atomList.end(); ++ia) { | |
388 | int atom1 = (*ia); | |
389 | atid = idents[atom1]; | |
390 | < | if (atypeCutoff[atid] > groupCutoff[cg1]) { |
390 | > | if (atypeCutoff[atid] > groupCutoff[cg1]) |
391 | groupCutoff[cg1] = atypeCutoff[atid]; | |
325 | – | } |
392 | } | |
393 | < | |
393 | > | |
394 | bool gTypeFound = false; | |
395 | for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { | |
396 | if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) { | |
# | Line 332 | Line 398 | namespace OpenMD { | |
398 | gTypeFound = true; | |
399 | } | |
400 | } | |
401 | < | if (!gTypeFound) { |
401 | > | if (!gTypeFound) { |
402 | gTypeCutoffs.push_back( groupCutoff[cg1] ); | |
403 | groupToGtype[cg1] = gTypeCutoffs.size() - 1; | |
404 | } | |
# | Line 341 | Line 407 | namespace OpenMD { | |
407 | ||
408 | // Now we find the maximum group cutoff value present in the simulation | |
409 | ||
410 | < | RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
410 | > | RealType groupMax = *max_element(gTypeCutoffs.begin(), |
411 | > | gTypeCutoffs.end()); |
412 | ||
413 | #ifdef IS_MPI | |
414 | < | MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX); |
414 | > | MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, |
415 | > | MPI::MAX); |
416 | #endif | |
417 | ||
418 | RealType tradRcut = groupMax; | |
# | Line 374 | Line 442 | namespace OpenMD { | |
442 | ||
443 | pair<int,int> key = make_pair(i,j); | |
444 | gTypeCutoffMap[key].first = thisRcut; | |
377 | – | |
445 | if (thisRcut > largestRcut_) largestRcut_ = thisRcut; | |
379 | – | |
446 | gTypeCutoffMap[key].second = thisRcut*thisRcut; | |
381 | – | |
447 | gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); | |
383 | – | |
448 | // sanity check | |
449 | ||
450 | if (userChoseCutoff_) { | |
# | Line 397 | Line 461 | namespace OpenMD { | |
461 | } | |
462 | } | |
463 | ||
400 | – | |
464 | groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) { | |
465 | int i, j; | |
466 | #ifdef IS_MPI | |
# | Line 440 | Line 503 | namespace OpenMD { | |
503 | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); | |
504 | ||
505 | if (storageLayout_ & DataStorage::dslParticlePot) { | |
506 | < | fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0); |
507 | < | fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0); |
506 | > | fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), |
507 | > | 0.0); |
508 | > | fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), |
509 | > | 0.0); |
510 | } | |
511 | ||
512 | if (storageLayout_ & DataStorage::dslDensity) { | |
# | Line 450 | Line 515 | namespace OpenMD { | |
515 | } | |
516 | ||
517 | if (storageLayout_ & DataStorage::dslFunctional) { | |
518 | < | fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0); |
519 | < | fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0); |
518 | > | fill(atomRowData.functional.begin(), atomRowData.functional.end(), |
519 | > | 0.0); |
520 | > | fill(atomColData.functional.begin(), atomColData.functional.end(), |
521 | > | 0.0); |
522 | } | |
523 | ||
524 | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { | |
# | Line 468 | Line 535 | namespace OpenMD { | |
535 | atomColData.skippedCharge.end(), 0.0); | |
536 | } | |
537 | ||
538 | < | #else |
539 | < | |
538 | > | if (storageLayout_ & DataStorage::dslFlucQForce) { |
539 | > | fill(atomRowData.flucQFrc.begin(), |
540 | > | atomRowData.flucQFrc.end(), 0.0); |
541 | > | fill(atomColData.flucQFrc.begin(), |
542 | > | atomColData.flucQFrc.end(), 0.0); |
543 | > | } |
544 | > | |
545 | > | if (storageLayout_ & DataStorage::dslElectricField) { |
546 | > | fill(atomRowData.electricField.begin(), |
547 | > | atomRowData.electricField.end(), V3Zero); |
548 | > | fill(atomColData.electricField.begin(), |
549 | > | atomColData.electricField.end(), V3Zero); |
550 | > | } |
551 | > | |
552 | > | if (storageLayout_ & DataStorage::dslFlucQForce) { |
553 | > | fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(), |
554 | > | 0.0); |
555 | > | fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(), |
556 | > | 0.0); |
557 | > | } |
558 | > | |
559 | > | #endif |
560 | > | // even in parallel, we need to zero out the local arrays: |
561 | > | |
562 | if (storageLayout_ & DataStorage::dslParticlePot) { | |
563 | fill(snap_->atomData.particlePot.begin(), | |
564 | snap_->atomData.particlePot.end(), 0.0); | |
# | Line 479 | Line 568 | namespace OpenMD { | |
568 | fill(snap_->atomData.density.begin(), | |
569 | snap_->atomData.density.end(), 0.0); | |
570 | } | |
571 | + | |
572 | if (storageLayout_ & DataStorage::dslFunctional) { | |
573 | fill(snap_->atomData.functional.begin(), | |
574 | snap_->atomData.functional.end(), 0.0); | |
575 | } | |
576 | + | |
577 | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { | |
578 | fill(snap_->atomData.functionalDerivative.begin(), | |
579 | snap_->atomData.functionalDerivative.end(), 0.0); | |
580 | } | |
581 | + | |
582 | if (storageLayout_ & DataStorage::dslSkippedCharge) { | |
583 | fill(snap_->atomData.skippedCharge.begin(), | |
584 | snap_->atomData.skippedCharge.end(), 0.0); | |
585 | } | |
586 | < | #endif |
587 | < | |
586 | > | |
587 | > | if (storageLayout_ & DataStorage::dslElectricField) { |
588 | > | fill(snap_->atomData.electricField.begin(), |
589 | > | snap_->atomData.electricField.end(), V3Zero); |
590 | > | } |
591 | } | |
592 | ||
593 | ||
# | Line 502 | Line 597 | namespace OpenMD { | |
597 | #ifdef IS_MPI | |
598 | ||
599 | // gather up the atomic positions | |
600 | < | AtomCommVectorRow->gather(snap_->atomData.position, |
600 | > | AtomPlanVectorRow->gather(snap_->atomData.position, |
601 | atomRowData.position); | |
602 | < | AtomCommVectorColumn->gather(snap_->atomData.position, |
602 | > | AtomPlanVectorColumn->gather(snap_->atomData.position, |
603 | atomColData.position); | |
604 | ||
605 | // gather up the cutoff group positions | |
606 | < | cgCommVectorRow->gather(snap_->cgData.position, |
606 | > | |
607 | > | cgPlanVectorRow->gather(snap_->cgData.position, |
608 | cgRowData.position); | |
609 | < | cgCommVectorColumn->gather(snap_->cgData.position, |
609 | > | |
610 | > | cgPlanVectorColumn->gather(snap_->cgData.position, |
611 | cgColData.position); | |
612 | + | |
613 | + | |
614 | + | |
615 | + | if (needVelocities_) { |
616 | + | // gather up the atomic velocities |
617 | + | AtomPlanVectorColumn->gather(snap_->atomData.velocity, |
618 | + | atomColData.velocity); |
619 | + | |
620 | + | cgPlanVectorColumn->gather(snap_->cgData.velocity, |
621 | + | cgColData.velocity); |
622 | + | } |
623 | + | |
624 | ||
625 | // if needed, gather the atomic rotation matrices | |
626 | if (storageLayout_ & DataStorage::dslAmat) { | |
627 | < | AtomCommMatrixRow->gather(snap_->atomData.aMat, |
627 | > | AtomPlanMatrixRow->gather(snap_->atomData.aMat, |
628 | atomRowData.aMat); | |
629 | < | AtomCommMatrixColumn->gather(snap_->atomData.aMat, |
629 | > | AtomPlanMatrixColumn->gather(snap_->atomData.aMat, |
630 | atomColData.aMat); | |
631 | } | |
632 | ||
633 | // if needed, gather the atomic eletrostatic frames | |
634 | if (storageLayout_ & DataStorage::dslElectroFrame) { | |
635 | < | AtomCommMatrixRow->gather(snap_->atomData.electroFrame, |
635 | > | AtomPlanMatrixRow->gather(snap_->atomData.electroFrame, |
636 | atomRowData.electroFrame); | |
637 | < | AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, |
637 | > | AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame, |
638 | atomColData.electroFrame); | |
639 | } | |
640 | + | |
641 | + | // if needed, gather the atomic fluctuating charge values |
642 | + | if (storageLayout_ & DataStorage::dslFlucQPosition) { |
643 | + | AtomPlanRealRow->gather(snap_->atomData.flucQPos, |
644 | + | atomRowData.flucQPos); |
645 | + | AtomPlanRealColumn->gather(snap_->atomData.flucQPos, |
646 | + | atomColData.flucQPos); |
647 | + | } |
648 | + | |
649 | #endif | |
650 | } | |
651 | ||
# | Line 541 | Line 659 | namespace OpenMD { | |
659 | ||
660 | if (storageLayout_ & DataStorage::dslDensity) { | |
661 | ||
662 | < | AtomCommRealRow->scatter(atomRowData.density, |
662 | > | AtomPlanRealRow->scatter(atomRowData.density, |
663 | snap_->atomData.density); | |
664 | ||
665 | int n = snap_->atomData.density.size(); | |
666 | vector<RealType> rho_tmp(n, 0.0); | |
667 | < | AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
667 | > | AtomPlanRealColumn->scatter(atomColData.density, rho_tmp); |
668 | for (int i = 0; i < n; i++) | |
669 | snap_->atomData.density[i] += rho_tmp[i]; | |
670 | } | |
671 | + | |
672 | + | if (storageLayout_ & DataStorage::dslElectricField) { |
673 | + | |
674 | + | AtomPlanVectorRow->scatter(atomRowData.electricField, |
675 | + | snap_->atomData.electricField); |
676 | + | |
677 | + | int n = snap_->atomData.electricField.size(); |
678 | + | vector<Vector3d> field_tmp(n, V3Zero); |
679 | + | AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp); |
680 | + | for (int i = 0; i < n; i++) |
681 | + | snap_->atomData.electricField[i] += field_tmp[i]; |
682 | + | } |
683 | #endif | |
684 | } | |
685 | ||
# | Line 562 | Line 692 | namespace OpenMD { | |
692 | storageLayout_ = sman_->getStorageLayout(); | |
693 | #ifdef IS_MPI | |
694 | if (storageLayout_ & DataStorage::dslFunctional) { | |
695 | < | AtomCommRealRow->gather(snap_->atomData.functional, |
695 | > | AtomPlanRealRow->gather(snap_->atomData.functional, |
696 | atomRowData.functional); | |
697 | < | AtomCommRealColumn->gather(snap_->atomData.functional, |
697 | > | AtomPlanRealColumn->gather(snap_->atomData.functional, |
698 | atomColData.functional); | |
699 | } | |
700 | ||
701 | if (storageLayout_ & DataStorage::dslFunctionalDerivative) { | |
702 | < | AtomCommRealRow->gather(snap_->atomData.functionalDerivative, |
702 | > | AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, |
703 | atomRowData.functionalDerivative); | |
704 | < | AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, |
704 | > | AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, |
705 | atomColData.functionalDerivative); | |
706 | } | |
707 | #endif | |
# | Line 585 | Line 715 | namespace OpenMD { | |
715 | int n = snap_->atomData.force.size(); | |
716 | vector<Vector3d> frc_tmp(n, V3Zero); | |
717 | ||
718 | < | AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); |
718 | > | AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp); |
719 | for (int i = 0; i < n; i++) { | |
720 | snap_->atomData.force[i] += frc_tmp[i]; | |
721 | frc_tmp[i] = 0.0; | |
722 | } | |
723 | ||
724 | < | AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); |
725 | < | for (int i = 0; i < n; i++) |
724 | > | AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp); |
725 | > | for (int i = 0; i < n; i++) { |
726 | snap_->atomData.force[i] += frc_tmp[i]; | |
727 | < | |
728 | < | |
727 | > | } |
728 | > | |
729 | if (storageLayout_ & DataStorage::dslTorque) { | |
730 | ||
731 | int nt = snap_->atomData.torque.size(); | |
732 | vector<Vector3d> trq_tmp(nt, V3Zero); | |
733 | ||
734 | < | AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
734 | > | AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp); |
735 | for (int i = 0; i < nt; i++) { | |
736 | snap_->atomData.torque[i] += trq_tmp[i]; | |
737 | trq_tmp[i] = 0.0; | |
738 | } | |
739 | ||
740 | < | AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
740 | > | AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp); |
741 | for (int i = 0; i < nt; i++) | |
742 | snap_->atomData.torque[i] += trq_tmp[i]; | |
743 | } | |
# | Line 617 | Line 747 | namespace OpenMD { | |
747 | int ns = snap_->atomData.skippedCharge.size(); | |
748 | vector<RealType> skch_tmp(ns, 0.0); | |
749 | ||
750 | < | AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
750 | > | AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
751 | for (int i = 0; i < ns; i++) { | |
752 | < | snap_->atomData.skippedCharge[i] = skch_tmp[i]; |
752 | > | snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
753 | skch_tmp[i] = 0.0; | |
754 | } | |
755 | ||
756 | < | AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
757 | < | for (int i = 0; i < ns; i++) |
756 | > | AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
757 | > | for (int i = 0; i < ns; i++) |
758 | snap_->atomData.skippedCharge[i] += skch_tmp[i]; | |
759 | + | |
760 | } | |
761 | ||
762 | + | if (storageLayout_ & DataStorage::dslFlucQForce) { |
763 | + | |
764 | + | int nq = snap_->atomData.flucQFrc.size(); |
765 | + | vector<RealType> fqfrc_tmp(nq, 0.0); |
766 | + | |
767 | + | AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp); |
768 | + | for (int i = 0; i < nq; i++) { |
769 | + | snap_->atomData.flucQFrc[i] += fqfrc_tmp[i]; |
770 | + | fqfrc_tmp[i] = 0.0; |
771 | + | } |
772 | + | |
773 | + | AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp); |
774 | + | for (int i = 0; i < nq; i++) |
775 | + | snap_->atomData.flucQFrc[i] += fqfrc_tmp[i]; |
776 | + | |
777 | + | } |
778 | + | |
779 | nLocal_ = snap_->getNumberOfAtoms(); | |
780 | ||
781 | vector<potVec> pot_temp(nLocal_, | |
# | Line 635 | Line 783 | namespace OpenMD { | |
783 | ||
784 | // scatter/gather pot_row into the members of my column | |
785 | ||
786 | < | AtomCommPotRow->scatter(pot_row, pot_temp); |
786 | > | AtomPlanPotRow->scatter(pot_row, pot_temp); |
787 | ||
788 | for (int ii = 0; ii < pot_temp.size(); ii++ ) | |
789 | pairwisePot += pot_temp[ii]; | |
790 | < | |
790 | > | |
791 | > | if (storageLayout_ & DataStorage::dslParticlePot) { |
792 | > | // This is the pairwise contribution to the particle pot. The |
793 | > | // embedding contribution is added in each of the low level |
794 | > | // non-bonded routines. In single processor, this is done in |
795 | > | // unpackInteractionData, not in collectData. |
796 | > | for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
797 | > | for (int i = 0; i < nLocal_; i++) { |
798 | > | // factor of two is because the total potential terms are divided |
799 | > | // by 2 in parallel due to row/ column scatter |
800 | > | snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii); |
801 | > | } |
802 | > | } |
803 | > | } |
804 | > | |
805 | fill(pot_temp.begin(), pot_temp.end(), | |
806 | Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); | |
807 | ||
808 | < | AtomCommPotColumn->scatter(pot_col, pot_temp); |
808 | > | AtomPlanPotColumn->scatter(pot_col, pot_temp); |
809 | ||
810 | for (int ii = 0; ii < pot_temp.size(); ii++ ) | |
811 | pairwisePot += pot_temp[ii]; | |
812 | + | |
813 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
814 | + | // This is the pairwise contribution to the particle pot. The |
815 | + | // embedding contribution is added in each of the low level |
816 | + | // non-bonded routines. In single processor, this is done in |
817 | + | // unpackInteractionData, not in collectData. |
818 | + | for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
819 | + | for (int i = 0; i < nLocal_; i++) { |
820 | + | // factor of two is because the total potential terms are divided |
821 | + | // by 2 in parallel due to row/ column scatter |
822 | + | snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii); |
823 | + | } |
824 | + | } |
825 | + | } |
826 | + | |
827 | + | if (storageLayout_ & DataStorage::dslParticlePot) { |
828 | + | int npp = snap_->atomData.particlePot.size(); |
829 | + | vector<RealType> ppot_temp(npp, 0.0); |
830 | + | |
831 | + | // This is the direct or embedding contribution to the particle |
832 | + | // pot. |
833 | + | |
834 | + | AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp); |
835 | + | for (int i = 0; i < npp; i++) { |
836 | + | snap_->atomData.particlePot[i] += ppot_temp[i]; |
837 | + | } |
838 | + | |
839 | + | fill(ppot_temp.begin(), ppot_temp.end(), 0.0); |
840 | + | |
841 | + | AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp); |
842 | + | for (int i = 0; i < npp; i++) { |
843 | + | snap_->atomData.particlePot[i] += ppot_temp[i]; |
844 | + | } |
845 | + | } |
846 | + | |
847 | + | for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
848 | + | RealType ploc1 = pairwisePot[ii]; |
849 | + | RealType ploc2 = 0.0; |
850 | + | MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
851 | + | pairwisePot[ii] = ploc2; |
852 | + | } |
853 | + | |
854 | + | // Here be dragons. |
855 | + | MPI::Intracomm col = colComm.getComm(); |
856 | + | |
857 | + | col.Allreduce(MPI::IN_PLACE, |
858 | + | &snap_->frameData.conductiveHeatFlux[0], 3, |
859 | + | MPI::REALTYPE, MPI::SUM); |
860 | + | |
861 | + | |
862 | #endif | |
863 | ||
864 | } | |
865 | ||
866 | + | /** |
867 | + | * Collects information obtained during the post-pair (and embedding |
868 | + | * functional) loops onto local data structures. |
869 | + | */ |
870 | + | void ForceMatrixDecomposition::collectSelfData() { |
871 | + | snap_ = sman_->getCurrentSnapshot(); |
872 | + | storageLayout_ = sman_->getStorageLayout(); |
873 | + | |
874 | + | #ifdef IS_MPI |
875 | + | for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
876 | + | RealType ploc1 = embeddingPot[ii]; |
877 | + | RealType ploc2 = 0.0; |
878 | + | MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
879 | + | embeddingPot[ii] = ploc2; |
880 | + | } |
881 | + | #endif |
882 | + | |
883 | + | } |
884 | + | |
885 | + | |
886 | + | |
887 | int ForceMatrixDecomposition::getNAtomsInRow() { | |
888 | #ifdef IS_MPI | |
889 | return nAtomsInRow_; | |
# | Line 691 | Line 924 | namespace OpenMD { | |
924 | return d; | |
925 | } | |
926 | ||
927 | + | Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){ |
928 | + | #ifdef IS_MPI |
929 | + | return cgColData.velocity[cg2]; |
930 | + | #else |
931 | + | return snap_->cgData.velocity[cg2]; |
932 | + | #endif |
933 | + | } |
934 | ||
935 | + | Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){ |
936 | + | #ifdef IS_MPI |
937 | + | return atomColData.velocity[atom2]; |
938 | + | #else |
939 | + | return snap_->atomData.velocity[atom2]; |
940 | + | #endif |
941 | + | } |
942 | + | |
943 | + | |
944 | Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){ | |
945 | ||
946 | Vector3d d; | |
# | Line 757 | Line 1006 | namespace OpenMD { | |
1006 | * We need to exclude some overcounted interactions that result from | |
1007 | * the parallel decomposition. | |
1008 | */ | |
1009 | < | bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
1010 | < | int unique_id_1, unique_id_2; |
1011 | < | |
1009 | > | bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) { |
1010 | > | int unique_id_1, unique_id_2, group1, group2; |
1011 | > | |
1012 | #ifdef IS_MPI | |
1013 | // in MPI, we have to look up the unique IDs for each atom | |
1014 | unique_id_1 = AtomRowToGlobal[atom1]; | |
1015 | unique_id_2 = AtomColToGlobal[atom2]; | |
1016 | < | |
1017 | < | // this situation should only arise in MPI simulations |
1016 | > | group1 = cgRowToGlobal[cg1]; |
1017 | > | group2 = cgColToGlobal[cg2]; |
1018 | > | #else |
1019 | > | unique_id_1 = AtomLocalToGlobal[atom1]; |
1020 | > | unique_id_2 = AtomLocalToGlobal[atom2]; |
1021 | > | group1 = cgLocalToGlobal[cg1]; |
1022 | > | group2 = cgLocalToGlobal[cg2]; |
1023 | > | #endif |
1024 | > | |
1025 | if (unique_id_1 == unique_id_2) return true; | |
1026 | < | |
1026 | > | |
1027 | > | #ifdef IS_MPI |
1028 | // this prevents us from doing the pair on multiple processors | |
1029 | if (unique_id_1 < unique_id_2) { | |
1030 | if ((unique_id_1 + unique_id_2) % 2 == 0) return true; | |
1031 | } else { | |
1032 | < | if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
1032 | > | if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
1033 | } | |
1034 | + | #endif |
1035 | + | |
1036 | + | #ifndef IS_MPI |
1037 | + | if (group1 == group2) { |
1038 | + | if (unique_id_1 < unique_id_2) return true; |
1039 | + | } |
1040 | #endif | |
1041 | + | |
1042 | return false; | |
1043 | } | |
1044 | ||
# | Line 788 | Line 1052 | namespace OpenMD { | |
1052 | * field) must still be handled for these pairs. | |
1053 | */ | |
1054 | bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { | |
1055 | < | int unique_id_2; |
1055 | > | |
1056 | > | // excludesForAtom was constructed to use row/column indices in the MPI |
1057 | > | // version, and to use local IDs in the non-MPI version: |
1058 | ||
793 | – | #ifdef IS_MPI |
794 | – | // in MPI, we have to look up the unique IDs for the row atom. |
795 | – | unique_id_2 = AtomColToGlobal[atom2]; |
796 | – | #else |
797 | – | // in the normal loop, the atom numbers are unique |
798 | – | unique_id_2 = atom2; |
799 | – | #endif |
800 | – | |
1059 | for (vector<int>::iterator i = excludesForAtom[atom1].begin(); | |
1060 | i != excludesForAtom[atom1].end(); ++i) { | |
1061 | < | if ( (*i) == unique_id_2 ) return true; |
1061 | > | if ( (*i) == atom2 ) return true; |
1062 | } | |
1063 | ||
1064 | return false; | |
# | Line 830 | Line 1088 | namespace OpenMD { | |
1088 | idat.excluded = excludeAtomPair(atom1, atom2); | |
1089 | ||
1090 | #ifdef IS_MPI | |
1091 | + | idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
1092 | + | //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
1093 | + | // ff_->getAtomType(identsCol[atom2]) ); |
1094 | ||
834 | – | idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
835 | – | ff_->getAtomType(identsCol[atom2]) ); |
836 | – | |
1095 | if (storageLayout_ & DataStorage::dslAmat) { | |
1096 | idat.A1 = &(atomRowData.aMat[atom1]); | |
1097 | idat.A2 = &(atomColData.aMat[atom2]); | |
# | Line 874 | Line 1132 | namespace OpenMD { | |
1132 | idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); | |
1133 | } | |
1134 | ||
1135 | + | if (storageLayout_ & DataStorage::dslFlucQPosition) { |
1136 | + | idat.flucQ1 = &(atomRowData.flucQPos[atom1]); |
1137 | + | idat.flucQ2 = &(atomColData.flucQPos[atom2]); |
1138 | + | } |
1139 | + | |
1140 | #else | |
1141 | + | |
1142 | + | idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
1143 | ||
879 | – | idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
880 | – | ff_->getAtomType(idents[atom2]) ); |
881 | – | |
1144 | if (storageLayout_ & DataStorage::dslAmat) { | |
1145 | idat.A1 = &(snap_->atomData.aMat[atom1]); | |
1146 | idat.A2 = &(snap_->atomData.aMat[atom2]); | |
# | Line 918 | Line 1180 | namespace OpenMD { | |
1180 | idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); | |
1181 | idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); | |
1182 | } | |
1183 | + | |
1184 | + | if (storageLayout_ & DataStorage::dslFlucQPosition) { |
1185 | + | idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]); |
1186 | + | idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]); |
1187 | + | } |
1188 | + | |
1189 | #endif | |
1190 | } | |
1191 | ||
1192 | ||
1193 | void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { | |
1194 | #ifdef IS_MPI | |
1195 | < | pot_row[atom1] += 0.5 * *(idat.pot); |
1196 | < | pot_col[atom2] += 0.5 * *(idat.pot); |
1195 | > | pot_row[atom1] += RealType(0.5) * *(idat.pot); |
1196 | > | pot_col[atom2] += RealType(0.5) * *(idat.pot); |
1197 | ||
1198 | atomRowData.force[atom1] += *(idat.f1); | |
1199 | atomColData.force[atom2] -= *(idat.f1); | |
1200 | + | |
1201 | + | if (storageLayout_ & DataStorage::dslFlucQForce) { |
1202 | + | atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1); |
1203 | + | atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2); |
1204 | + | } |
1205 | + | |
1206 | + | if (storageLayout_ & DataStorage::dslElectricField) { |
1207 | + | atomRowData.electricField[atom1] += *(idat.eField1); |
1208 | + | atomColData.electricField[atom2] += *(idat.eField2); |
1209 | + | } |
1210 | + | |
1211 | #else | |
1212 | pairwisePot += *(idat.pot); | |
1213 | ||
1214 | snap_->atomData.force[atom1] += *(idat.f1); | |
1215 | snap_->atomData.force[atom2] -= *(idat.f1); | |
1216 | + | |
1217 | + | if (idat.doParticlePot) { |
1218 | + | // This is the pairwise contribution to the particle pot. The |
1219 | + | // embedding contribution is added in each of the low level |
1220 | + | // non-bonded routines. In parallel, this calculation is done |
1221 | + | // in collectData, not in unpackInteractionData. |
1222 | + | snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw); |
1223 | + | snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw); |
1224 | + | } |
1225 | + | |
1226 | + | if (storageLayout_ & DataStorage::dslFlucQForce) { |
1227 | + | snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1); |
1228 | + | snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2); |
1229 | + | } |
1230 | + | |
1231 | + | if (storageLayout_ & DataStorage::dslElectricField) { |
1232 | + | snap_->atomData.electricField[atom1] += *(idat.eField1); |
1233 | + | snap_->atomData.electricField[atom2] += *(idat.eField2); |
1234 | + | } |
1235 | + | |
1236 | #endif | |
1237 | ||
1238 | } | |
# | Line 1015 | Line 1314 | namespace OpenMD { | |
1314 | // add this cutoff group to the list of groups in this cell; | |
1315 | cellListRow_[cellIndex].push_back(i); | |
1316 | } | |
1018 | – | |
1317 | for (int i = 0; i < nGroupsInCol_; i++) { | |
1318 | rs = cgColData.position[i]; | |
1319 | ||
# | Line 1040 | Line 1338 | namespace OpenMD { | |
1338 | // add this cutoff group to the list of groups in this cell; | |
1339 | cellListCol_[cellIndex].push_back(i); | |
1340 | } | |
1341 | + | |
1342 | #else | |
1343 | for (int i = 0; i < nGroups_; i++) { | |
1344 | rs = snap_->cgData.position[i]; | |
# | Line 1060 | Line 1359 | namespace OpenMD { | |
1359 | whichCell.z() = nCells_.z() * scaled.z(); | |
1360 | ||
1361 | // find single index of this cell: | |
1362 | < | cellIndex = Vlinear(whichCell, nCells_); |
1362 | > | cellIndex = Vlinear(whichCell, nCells_); |
1363 | ||
1364 | // add this cutoff group to the list of groups in this cell; | |
1365 | cellList_[cellIndex].push_back(i); | |
1366 | } | |
1367 | + | |
1368 | #endif | |
1369 | ||
1370 | for (int m1z = 0; m1z < nCells_.z(); m1z++) { | |
# | Line 1077 | Line 1377 | namespace OpenMD { | |
1377 | os != cellOffsets_.end(); ++os) { | |
1378 | ||
1379 | Vector3i m2v = m1v + (*os); | |
1380 | < | |
1380 | > | |
1381 | > | |
1382 | if (m2v.x() >= nCells_.x()) { | |
1383 | m2v.x() = 0; | |
1384 | } else if (m2v.x() < 0) { | |
# | Line 1095 | Line 1396 | namespace OpenMD { | |
1396 | } else if (m2v.z() < 0) { | |
1397 | m2v.z() = nCells_.z() - 1; | |
1398 | } | |
1399 | < | |
1399 | > | |
1400 | int m2 = Vlinear (m2v, nCells_); | |
1401 | ||
1402 | #ifdef IS_MPI | |
# | Line 1104 | Line 1405 | namespace OpenMD { | |
1405 | for (vector<int>::iterator j2 = cellListCol_[m2].begin(); | |
1406 | j2 != cellListCol_[m2].end(); ++j2) { | |
1407 | ||
1408 | < | // Always do this if we're in different cells or if |
1409 | < | // we're in the same cell and the global index of the |
1410 | < | // j2 cutoff group is less than the j1 cutoff group |
1411 | < | |
1412 | < | if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
1413 | < | dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
1414 | < | snap_->wrapVector(dr); |
1415 | < | cuts = getGroupCutoffs( (*j1), (*j2) ); |
1416 | < | if (dr.lengthSquare() < cuts.third) { |
1116 | < | neighborList.push_back(make_pair((*j1), (*j2))); |
1117 | < | } |
1118 | < | } |
1408 | > | // In parallel, we need to visit *all* pairs of row |
1409 | > | // & column indicies and will divide labor in the |
1410 | > | // force evaluation later. |
1411 | > | dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
1412 | > | snap_->wrapVector(dr); |
1413 | > | cuts = getGroupCutoffs( (*j1), (*j2) ); |
1414 | > | if (dr.lengthSquare() < cuts.third) { |
1415 | > | neighborList.push_back(make_pair((*j1), (*j2))); |
1416 | > | } |
1417 | } | |
1418 | } | |
1419 | #else | |
1122 | – | |
1420 | for (vector<int>::iterator j1 = cellList_[m1].begin(); | |
1421 | j1 != cellList_[m1].end(); ++j1) { | |
1422 | for (vector<int>::iterator j2 = cellList_[m2].begin(); | |
1423 | j2 != cellList_[m2].end(); ++j2) { | |
1424 | < | |
1424 | > | |
1425 | // Always do this if we're in different cells or if | |
1426 | < | // we're in the same cell and the global index of the |
1427 | < | // j2 cutoff group is less than the j1 cutoff group |
1428 | < | |
1429 | < | if (m2 != m1 || (*j2) < (*j1)) { |
1426 | > | // we're in the same cell and the global index of |
1427 | > | // the j2 cutoff group is greater than or equal to |
1428 | > | // the j1 cutoff group. Note that Rappaport's code |
1429 | > | // has a "less than" conditional here, but that |
1430 | > | // deals with atom-by-atom computation. OpenMD |
1431 | > | // allows atoms within a single cutoff group to |
1432 | > | // interact with each other. |
1433 | > | |
1434 | > | |
1435 | > | |
1436 | > | if (m2 != m1 || (*j2) >= (*j1) ) { |
1437 | > | |
1438 | dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; | |
1439 | snap_->wrapVector(dr); | |
1440 | cuts = getGroupCutoffs( (*j1), (*j2) ); | |
# | Line 1148 | Line 1453 | namespace OpenMD { | |
1453 | // branch to do all cutoff group pairs | |
1454 | #ifdef IS_MPI | |
1455 | for (int j1 = 0; j1 < nGroupsInRow_; j1++) { | |
1456 | < | for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
1456 | > | for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
1457 | dr = cgColData.position[j2] - cgRowData.position[j1]; | |
1458 | snap_->wrapVector(dr); | |
1459 | cuts = getGroupCutoffs( j1, j2 ); | |
# | Line 1156 | Line 1461 | namespace OpenMD { | |
1461 | neighborList.push_back(make_pair(j1, j2)); | |
1462 | } | |
1463 | } | |
1464 | < | } |
1464 | > | } |
1465 | #else | |
1466 | < | for (int j1 = 0; j1 < nGroups_ - 1; j1++) { |
1467 | < | for (int j2 = j1 + 1; j2 < nGroups_; j2++) { |
1466 | > | // include all groups here. |
1467 | > | for (int j1 = 0; j1 < nGroups_; j1++) { |
1468 | > | // include self group interactions j2 == j1 |
1469 | > | for (int j2 = j1; j2 < nGroups_; j2++) { |
1470 | dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; | |
1471 | snap_->wrapVector(dr); | |
1472 | cuts = getGroupCutoffs( j1, j2 ); | |
1473 | if (dr.lengthSquare() < cuts.third) { | |
1474 | neighborList.push_back(make_pair(j1, j2)); | |
1475 | } | |
1476 | < | } |
1477 | < | } |
1476 | > | } |
1477 | > | } |
1478 | #endif | |
1479 | } | |
1480 |
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