| 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" |
| 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(); |
| 62 |
– |
cerr << "in dId, nGroups = " << nGroups_ << "\n"; |
| 100 |
|
// gather the information for atomtype IDs (atids): |
| 101 |
|
idents = info_->getIdentArray(); |
| 102 |
|
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 103 |
|
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 104 |
|
vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); |
| 105 |
+ |
|
| 106 |
|
massFactors = info_->getMassFactors(); |
| 69 |
– |
PairList excludes = info_->getExcludedInteractions(); |
| 70 |
– |
PairList oneTwo = info_->getOneTwoInteractions(); |
| 71 |
– |
PairList oneThree = info_->getOneThreeInteractions(); |
| 72 |
– |
PairList oneFour = info_->getOneFourInteractions(); |
| 107 |
|
|
| 108 |
+ |
PairList* excludes = info_->getExcludedInteractions(); |
| 109 |
+ |
PairList* oneTwo = info_->getOneTwoInteractions(); |
| 110 |
+ |
PairList* oneThree = info_->getOneThreeInteractions(); |
| 111 |
+ |
PairList* oneFour = info_->getOneFourInteractions(); |
| 112 |
+ |
|
| 113 |
|
#ifdef IS_MPI |
| 114 |
|
|
| 115 |
< |
AtomCommIntRow = new Communicator<Row,int>(nLocal_); |
| 116 |
< |
AtomCommRealRow = new Communicator<Row,RealType>(nLocal_); |
| 78 |
< |
AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_); |
| 79 |
< |
AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_); |
| 80 |
< |
AtomCommPotRow = new Communicator<Row,potVec>(nLocal_); |
| 115 |
> |
MPI::Intracomm row = rowComm.getComm(); |
| 116 |
> |
MPI::Intracomm col = colComm.getComm(); |
| 117 |
|
|
| 118 |
< |
AtomCommIntColumn = new Communicator<Column,int>(nLocal_); |
| 119 |
< |
AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_); |
| 120 |
< |
AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_); |
| 121 |
< |
AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_); |
| 122 |
< |
AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_); |
| 118 |
> |
AtomPlanIntRow = new Plan<int>(row, nLocal_); |
| 119 |
> |
AtomPlanRealRow = new Plan<RealType>(row, nLocal_); |
| 120 |
> |
AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_); |
| 121 |
> |
AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_); |
| 122 |
> |
AtomPlanPotRow = new Plan<potVec>(row, nLocal_); |
| 123 |
|
|
| 124 |
< |
cgCommIntRow = new Communicator<Row,int>(nGroups_); |
| 125 |
< |
cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_); |
| 126 |
< |
cgCommIntColumn = new Communicator<Column,int>(nGroups_); |
| 127 |
< |
cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_); |
| 124 |
> |
AtomPlanIntColumn = new Plan<int>(col, nLocal_); |
| 125 |
> |
AtomPlanRealColumn = new Plan<RealType>(col, nLocal_); |
| 126 |
> |
AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_); |
| 127 |
> |
AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_); |
| 128 |
> |
AtomPlanPotColumn = new Plan<potVec>(col, nLocal_); |
| 129 |
|
|
| 130 |
< |
nAtomsInRow_ = AtomCommIntRow->getSize(); |
| 131 |
< |
nAtomsInCol_ = AtomCommIntColumn->getSize(); |
| 132 |
< |
nGroupsInRow_ = cgCommIntRow->getSize(); |
| 133 |
< |
nGroupsInCol_ = cgCommIntColumn->getSize(); |
| 130 |
> |
cgPlanIntRow = new Plan<int>(row, nGroups_); |
| 131 |
> |
cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_); |
| 132 |
> |
cgPlanIntColumn = new Plan<int>(col, nGroups_); |
| 133 |
> |
cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_); |
| 134 |
|
|
| 135 |
+ |
nAtomsInRow_ = AtomPlanIntRow->getSize(); |
| 136 |
+ |
nAtomsInCol_ = AtomPlanIntColumn->getSize(); |
| 137 |
+ |
nGroupsInRow_ = cgPlanIntRow->getSize(); |
| 138 |
+ |
nGroupsInCol_ = cgPlanIntColumn->getSize(); |
| 139 |
+ |
|
| 140 |
|
// Modify the data storage objects with the correct layouts and sizes: |
| 141 |
|
atomRowData.resize(nAtomsInRow_); |
| 142 |
|
atomRowData.setStorageLayout(storageLayout_); |
| 150 |
|
identsRow.resize(nAtomsInRow_); |
| 151 |
|
identsCol.resize(nAtomsInCol_); |
| 152 |
|
|
| 153 |
< |
AtomCommIntRow->gather(idents, identsRow); |
| 154 |
< |
AtomCommIntColumn->gather(idents, identsCol); |
| 153 |
> |
AtomPlanIntRow->gather(idents, identsRow); |
| 154 |
> |
AtomPlanIntColumn->gather(idents, identsCol); |
| 155 |
|
|
| 156 |
< |
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 157 |
< |
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 158 |
< |
|
| 117 |
< |
cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 118 |
< |
cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 156 |
> |
// allocate memory for the parallel objects |
| 157 |
> |
atypesRow.resize(nAtomsInRow_); |
| 158 |
> |
atypesCol.resize(nAtomsInCol_); |
| 159 |
|
|
| 160 |
< |
AtomCommRealRow->gather(massFactors, massFactorsRow); |
| 161 |
< |
AtomCommRealColumn->gather(massFactors, massFactorsCol); |
| 160 |
> |
for (int i = 0; i < nAtomsInRow_; i++) |
| 161 |
> |
atypesRow[i] = ff_->getAtomType(identsRow[i]); |
| 162 |
> |
for (int i = 0; i < nAtomsInCol_; i++) |
| 163 |
> |
atypesCol[i] = ff_->getAtomType(identsCol[i]); |
| 164 |
|
|
| 165 |
+ |
pot_row.resize(nAtomsInRow_); |
| 166 |
+ |
pot_col.resize(nAtomsInCol_); |
| 167 |
+ |
|
| 168 |
+ |
AtomRowToGlobal.resize(nAtomsInRow_); |
| 169 |
+ |
AtomColToGlobal.resize(nAtomsInCol_); |
| 170 |
+ |
AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 171 |
+ |
AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 172 |
+ |
|
| 173 |
+ |
cgRowToGlobal.resize(nGroupsInRow_); |
| 174 |
+ |
cgColToGlobal.resize(nGroupsInCol_); |
| 175 |
+ |
cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 176 |
+ |
cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 177 |
+ |
|
| 178 |
+ |
massFactorsRow.resize(nAtomsInRow_); |
| 179 |
+ |
massFactorsCol.resize(nAtomsInCol_); |
| 180 |
+ |
AtomPlanRealRow->gather(massFactors, massFactorsRow); |
| 181 |
+ |
AtomPlanRealColumn->gather(massFactors, massFactorsCol); |
| 182 |
+ |
|
| 183 |
|
groupListRow_.clear(); |
| 184 |
|
groupListRow_.resize(nGroupsInRow_); |
| 185 |
|
for (int i = 0; i < nGroupsInRow_; i++) { |
| 202 |
|
} |
| 203 |
|
} |
| 204 |
|
|
| 205 |
< |
skipsForAtom.clear(); |
| 206 |
< |
skipsForAtom.resize(nAtomsInRow_); |
| 205 |
> |
excludesForAtom.clear(); |
| 206 |
> |
excludesForAtom.resize(nAtomsInRow_); |
| 207 |
|
toposForAtom.clear(); |
| 208 |
|
toposForAtom.resize(nAtomsInRow_); |
| 209 |
|
topoDist.clear(); |
| 214 |
|
for (int j = 0; j < nAtomsInCol_; j++) { |
| 215 |
|
int jglob = AtomColToGlobal[j]; |
| 216 |
|
|
| 217 |
< |
if (excludes.hasPair(iglob, jglob)) |
| 218 |
< |
skipsForAtom[i].push_back(j); |
| 217 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 218 |
> |
excludesForAtom[i].push_back(j); |
| 219 |
|
|
| 220 |
< |
if (oneTwo.hasPair(iglob, jglob)) { |
| 220 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 221 |
|
toposForAtom[i].push_back(j); |
| 222 |
|
topoDist[i].push_back(1); |
| 223 |
|
} else { |
| 224 |
< |
if (oneThree.hasPair(iglob, jglob)) { |
| 224 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 225 |
|
toposForAtom[i].push_back(j); |
| 226 |
|
topoDist[i].push_back(2); |
| 227 |
|
} else { |
| 228 |
< |
if (oneFour.hasPair(iglob, jglob)) { |
| 228 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 229 |
|
toposForAtom[i].push_back(j); |
| 230 |
|
topoDist[i].push_back(3); |
| 231 |
|
} |
| 234 |
|
} |
| 235 |
|
} |
| 236 |
|
|
| 237 |
< |
#endif |
| 238 |
< |
|
| 239 |
< |
groupList_.clear(); |
| 180 |
< |
groupList_.resize(nGroups_); |
| 181 |
< |
for (int i = 0; i < nGroups_; i++) { |
| 182 |
< |
int gid = cgLocalToGlobal[i]; |
| 183 |
< |
for (int j = 0; j < nLocal_; j++) { |
| 184 |
< |
int aid = AtomLocalToGlobal[j]; |
| 185 |
< |
if (globalGroupMembership[aid] == gid) { |
| 186 |
< |
groupList_[i].push_back(j); |
| 187 |
< |
} |
| 188 |
< |
} |
| 189 |
< |
} |
| 190 |
< |
|
| 191 |
< |
skipsForAtom.clear(); |
| 192 |
< |
skipsForAtom.resize(nLocal_); |
| 237 |
> |
#else |
| 238 |
> |
excludesForAtom.clear(); |
| 239 |
> |
excludesForAtom.resize(nLocal_); |
| 240 |
|
toposForAtom.clear(); |
| 241 |
|
toposForAtom.resize(nLocal_); |
| 242 |
|
topoDist.clear(); |
| 248 |
|
for (int j = 0; j < nLocal_; j++) { |
| 249 |
|
int jglob = AtomLocalToGlobal[j]; |
| 250 |
|
|
| 251 |
< |
if (excludes.hasPair(iglob, jglob)) |
| 252 |
< |
skipsForAtom[i].push_back(j); |
| 251 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 252 |
> |
excludesForAtom[i].push_back(j); |
| 253 |
|
|
| 254 |
< |
if (oneTwo.hasPair(iglob, jglob)) { |
| 254 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 255 |
|
toposForAtom[i].push_back(j); |
| 256 |
|
topoDist[i].push_back(1); |
| 257 |
|
} else { |
| 258 |
< |
if (oneThree.hasPair(iglob, jglob)) { |
| 258 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 259 |
|
toposForAtom[i].push_back(j); |
| 260 |
|
topoDist[i].push_back(2); |
| 261 |
|
} else { |
| 262 |
< |
if (oneFour.hasPair(iglob, jglob)) { |
| 262 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 263 |
|
toposForAtom[i].push_back(j); |
| 264 |
|
topoDist[i].push_back(3); |
| 265 |
|
} |
| 267 |
|
} |
| 268 |
|
} |
| 269 |
|
} |
| 270 |
< |
|
| 270 |
> |
#endif |
| 271 |
> |
|
| 272 |
> |
// allocate memory for the parallel objects |
| 273 |
> |
atypesLocal.resize(nLocal_); |
| 274 |
> |
|
| 275 |
> |
for (int i = 0; i < nLocal_; i++) |
| 276 |
> |
atypesLocal[i] = ff_->getAtomType(idents[i]); |
| 277 |
> |
|
| 278 |
> |
groupList_.clear(); |
| 279 |
> |
groupList_.resize(nGroups_); |
| 280 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 281 |
> |
int gid = cgLocalToGlobal[i]; |
| 282 |
> |
for (int j = 0; j < nLocal_; j++) { |
| 283 |
> |
int aid = AtomLocalToGlobal[j]; |
| 284 |
> |
if (globalGroupMembership[aid] == gid) { |
| 285 |
> |
groupList_[i].push_back(j); |
| 286 |
> |
} |
| 287 |
> |
} |
| 288 |
> |
} |
| 289 |
> |
|
| 290 |
> |
|
| 291 |
|
createGtypeCutoffMap(); |
| 292 |
+ |
|
| 293 |
|
} |
| 294 |
|
|
| 295 |
|
void ForceMatrixDecomposition::createGtypeCutoffMap() { |
| 296 |
< |
|
| 296 |
> |
|
| 297 |
|
RealType tol = 1e-6; |
| 298 |
+ |
largestRcut_ = 0.0; |
| 299 |
|
RealType rc; |
| 300 |
|
int atid; |
| 301 |
|
set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
| 302 |
< |
vector<RealType> atypeCutoff; |
| 303 |
< |
atypeCutoff.resize( atypes.size() ); |
| 302 |
> |
|
| 303 |
> |
map<int, RealType> atypeCutoff; |
| 304 |
|
|
| 305 |
|
for (set<AtomType*>::iterator at = atypes.begin(); |
| 306 |
|
at != atypes.end(); ++at){ |
| 307 |
|
atid = (*at)->getIdent(); |
| 308 |
< |
|
| 240 |
< |
if (userChoseCutoff_) |
| 308 |
> |
if (userChoseCutoff_) |
| 309 |
|
atypeCutoff[atid] = userCutoff_; |
| 310 |
|
else |
| 311 |
|
atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
| 312 |
|
} |
| 313 |
< |
|
| 313 |
> |
|
| 314 |
|
vector<RealType> gTypeCutoffs; |
| 247 |
– |
|
| 315 |
|
// first we do a single loop over the cutoff groups to find the |
| 316 |
|
// largest cutoff for any atypes present in this group. |
| 317 |
|
#ifdef IS_MPI |
| 369 |
|
|
| 370 |
|
vector<RealType> groupCutoff(nGroups_, 0.0); |
| 371 |
|
groupToGtype.resize(nGroups_); |
| 305 |
– |
|
| 306 |
– |
cerr << "nGroups = " << nGroups_ << "\n"; |
| 372 |
|
for (int cg1 = 0; cg1 < nGroups_; cg1++) { |
| 308 |
– |
|
| 373 |
|
groupCutoff[cg1] = 0.0; |
| 374 |
|
vector<int> atomList = getAtomsInGroupRow(cg1); |
| 311 |
– |
|
| 375 |
|
for (vector<int>::iterator ia = atomList.begin(); |
| 376 |
|
ia != atomList.end(); ++ia) { |
| 377 |
|
int atom1 = (*ia); |
| 378 |
|
atid = idents[atom1]; |
| 379 |
< |
if (atypeCutoff[atid] > groupCutoff[cg1]) { |
| 379 |
> |
if (atypeCutoff[atid] > groupCutoff[cg1]) |
| 380 |
|
groupCutoff[cg1] = atypeCutoff[atid]; |
| 318 |
– |
} |
| 381 |
|
} |
| 382 |
< |
|
| 382 |
> |
|
| 383 |
|
bool gTypeFound = false; |
| 384 |
|
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
| 385 |
|
if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) { |
| 387 |
|
gTypeFound = true; |
| 388 |
|
} |
| 389 |
|
} |
| 390 |
< |
if (!gTypeFound) { |
| 390 |
> |
if (!gTypeFound) { |
| 391 |
|
gTypeCutoffs.push_back( groupCutoff[cg1] ); |
| 392 |
|
groupToGtype[cg1] = gTypeCutoffs.size() - 1; |
| 393 |
|
} |
| 394 |
|
} |
| 395 |
|
#endif |
| 396 |
|
|
| 335 |
– |
cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n"; |
| 397 |
|
// Now we find the maximum group cutoff value present in the simulation |
| 398 |
|
|
| 399 |
< |
RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
| 399 |
> |
RealType groupMax = *max_element(gTypeCutoffs.begin(), |
| 400 |
> |
gTypeCutoffs.end()); |
| 401 |
|
|
| 402 |
|
#ifdef IS_MPI |
| 403 |
< |
MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX); |
| 403 |
> |
MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, |
| 404 |
> |
MPI::MAX); |
| 405 |
|
#endif |
| 406 |
|
|
| 407 |
|
RealType tradRcut = groupMax; |
| 431 |
|
|
| 432 |
|
pair<int,int> key = make_pair(i,j); |
| 433 |
|
gTypeCutoffMap[key].first = thisRcut; |
| 371 |
– |
|
| 434 |
|
if (thisRcut > largestRcut_) largestRcut_ = thisRcut; |
| 373 |
– |
|
| 435 |
|
gTypeCutoffMap[key].second = thisRcut*thisRcut; |
| 375 |
– |
|
| 436 |
|
gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); |
| 377 |
– |
|
| 437 |
|
// sanity check |
| 438 |
|
|
| 439 |
|
if (userChoseCutoff_) { |
| 493 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 494 |
|
|
| 495 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 496 |
< |
fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0); |
| 497 |
< |
fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0); |
| 496 |
> |
fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), |
| 497 |
> |
0.0); |
| 498 |
> |
fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), |
| 499 |
> |
0.0); |
| 500 |
|
} |
| 501 |
|
|
| 502 |
|
if (storageLayout_ & DataStorage::dslDensity) { |
| 505 |
|
} |
| 506 |
|
|
| 507 |
|
if (storageLayout_ & DataStorage::dslFunctional) { |
| 508 |
< |
fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0); |
| 509 |
< |
fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0); |
| 508 |
> |
fill(atomRowData.functional.begin(), atomRowData.functional.end(), |
| 509 |
> |
0.0); |
| 510 |
> |
fill(atomColData.functional.begin(), atomColData.functional.end(), |
| 511 |
> |
0.0); |
| 512 |
|
} |
| 513 |
|
|
| 514 |
|
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 518 |
|
atomColData.functionalDerivative.end(), 0.0); |
| 519 |
|
} |
| 520 |
|
|
| 521 |
< |
#else |
| 522 |
< |
|
| 521 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 522 |
> |
fill(atomRowData.skippedCharge.begin(), |
| 523 |
> |
atomRowData.skippedCharge.end(), 0.0); |
| 524 |
> |
fill(atomColData.skippedCharge.begin(), |
| 525 |
> |
atomColData.skippedCharge.end(), 0.0); |
| 526 |
> |
} |
| 527 |
> |
|
| 528 |
> |
#endif |
| 529 |
> |
// even in parallel, we need to zero out the local arrays: |
| 530 |
> |
|
| 531 |
|
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 532 |
|
fill(snap_->atomData.particlePot.begin(), |
| 533 |
|
snap_->atomData.particlePot.end(), 0.0); |
| 545 |
|
fill(snap_->atomData.functionalDerivative.begin(), |
| 546 |
|
snap_->atomData.functionalDerivative.end(), 0.0); |
| 547 |
|
} |
| 548 |
< |
#endif |
| 548 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 549 |
> |
fill(snap_->atomData.skippedCharge.begin(), |
| 550 |
> |
snap_->atomData.skippedCharge.end(), 0.0); |
| 551 |
> |
} |
| 552 |
|
|
| 553 |
|
} |
| 554 |
|
|
| 559 |
|
#ifdef IS_MPI |
| 560 |
|
|
| 561 |
|
// gather up the atomic positions |
| 562 |
< |
AtomCommVectorRow->gather(snap_->atomData.position, |
| 562 |
> |
AtomPlanVectorRow->gather(snap_->atomData.position, |
| 563 |
|
atomRowData.position); |
| 564 |
< |
AtomCommVectorColumn->gather(snap_->atomData.position, |
| 564 |
> |
AtomPlanVectorColumn->gather(snap_->atomData.position, |
| 565 |
|
atomColData.position); |
| 566 |
|
|
| 567 |
|
// gather up the cutoff group positions |
| 568 |
< |
cgCommVectorRow->gather(snap_->cgData.position, |
| 568 |
> |
|
| 569 |
> |
cgPlanVectorRow->gather(snap_->cgData.position, |
| 570 |
|
cgRowData.position); |
| 571 |
< |
cgCommVectorColumn->gather(snap_->cgData.position, |
| 571 |
> |
|
| 572 |
> |
cgPlanVectorColumn->gather(snap_->cgData.position, |
| 573 |
|
cgColData.position); |
| 574 |
+ |
|
| 575 |
|
|
| 576 |
|
// if needed, gather the atomic rotation matrices |
| 577 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 578 |
< |
AtomCommMatrixRow->gather(snap_->atomData.aMat, |
| 578 |
> |
AtomPlanMatrixRow->gather(snap_->atomData.aMat, |
| 579 |
|
atomRowData.aMat); |
| 580 |
< |
AtomCommMatrixColumn->gather(snap_->atomData.aMat, |
| 580 |
> |
AtomPlanMatrixColumn->gather(snap_->atomData.aMat, |
| 581 |
|
atomColData.aMat); |
| 582 |
|
} |
| 583 |
|
|
| 584 |
|
// if needed, gather the atomic eletrostatic frames |
| 585 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 586 |
< |
AtomCommMatrixRow->gather(snap_->atomData.electroFrame, |
| 586 |
> |
AtomPlanMatrixRow->gather(snap_->atomData.electroFrame, |
| 587 |
|
atomRowData.electroFrame); |
| 588 |
< |
AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, |
| 588 |
> |
AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame, |
| 589 |
|
atomColData.electroFrame); |
| 590 |
|
} |
| 591 |
+ |
|
| 592 |
|
#endif |
| 593 |
|
} |
| 594 |
|
|
| 602 |
|
|
| 603 |
|
if (storageLayout_ & DataStorage::dslDensity) { |
| 604 |
|
|
| 605 |
< |
AtomCommRealRow->scatter(atomRowData.density, |
| 605 |
> |
AtomPlanRealRow->scatter(atomRowData.density, |
| 606 |
|
snap_->atomData.density); |
| 607 |
|
|
| 608 |
|
int n = snap_->atomData.density.size(); |
| 609 |
|
vector<RealType> rho_tmp(n, 0.0); |
| 610 |
< |
AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
| 610 |
> |
AtomPlanRealColumn->scatter(atomColData.density, rho_tmp); |
| 611 |
|
for (int i = 0; i < n; i++) |
| 612 |
|
snap_->atomData.density[i] += rho_tmp[i]; |
| 613 |
|
} |
| 623 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 624 |
|
#ifdef IS_MPI |
| 625 |
|
if (storageLayout_ & DataStorage::dslFunctional) { |
| 626 |
< |
AtomCommRealRow->gather(snap_->atomData.functional, |
| 626 |
> |
AtomPlanRealRow->gather(snap_->atomData.functional, |
| 627 |
|
atomRowData.functional); |
| 628 |
< |
AtomCommRealColumn->gather(snap_->atomData.functional, |
| 628 |
> |
AtomPlanRealColumn->gather(snap_->atomData.functional, |
| 629 |
|
atomColData.functional); |
| 630 |
|
} |
| 631 |
|
|
| 632 |
|
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 633 |
< |
AtomCommRealRow->gather(snap_->atomData.functionalDerivative, |
| 633 |
> |
AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, |
| 634 |
|
atomRowData.functionalDerivative); |
| 635 |
< |
AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, |
| 635 |
> |
AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, |
| 636 |
|
atomColData.functionalDerivative); |
| 637 |
|
} |
| 638 |
|
#endif |
| 646 |
|
int n = snap_->atomData.force.size(); |
| 647 |
|
vector<Vector3d> frc_tmp(n, V3Zero); |
| 648 |
|
|
| 649 |
< |
AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); |
| 649 |
> |
AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp); |
| 650 |
|
for (int i = 0; i < n; i++) { |
| 651 |
|
snap_->atomData.force[i] += frc_tmp[i]; |
| 652 |
|
frc_tmp[i] = 0.0; |
| 653 |
|
} |
| 654 |
|
|
| 655 |
< |
AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); |
| 656 |
< |
for (int i = 0; i < n; i++) |
| 655 |
> |
AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp); |
| 656 |
> |
for (int i = 0; i < n; i++) { |
| 657 |
|
snap_->atomData.force[i] += frc_tmp[i]; |
| 658 |
< |
|
| 659 |
< |
|
| 658 |
> |
} |
| 659 |
> |
|
| 660 |
|
if (storageLayout_ & DataStorage::dslTorque) { |
| 661 |
|
|
| 662 |
< |
int nt = snap_->atomData.force.size(); |
| 662 |
> |
int nt = snap_->atomData.torque.size(); |
| 663 |
|
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 664 |
|
|
| 665 |
< |
AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 666 |
< |
for (int i = 0; i < n; i++) { |
| 665 |
> |
AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 666 |
> |
for (int i = 0; i < nt; i++) { |
| 667 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 668 |
|
trq_tmp[i] = 0.0; |
| 669 |
|
} |
| 670 |
|
|
| 671 |
< |
AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 672 |
< |
for (int i = 0; i < n; i++) |
| 671 |
> |
AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 672 |
> |
for (int i = 0; i < nt; i++) |
| 673 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 674 |
|
} |
| 675 |
+ |
|
| 676 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 677 |
+ |
|
| 678 |
+ |
int ns = snap_->atomData.skippedCharge.size(); |
| 679 |
+ |
vector<RealType> skch_tmp(ns, 0.0); |
| 680 |
+ |
|
| 681 |
+ |
AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
| 682 |
+ |
for (int i = 0; i < ns; i++) { |
| 683 |
+ |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 684 |
+ |
skch_tmp[i] = 0.0; |
| 685 |
+ |
} |
| 686 |
+ |
|
| 687 |
+ |
AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
| 688 |
+ |
for (int i = 0; i < ns; i++) |
| 689 |
+ |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 690 |
+ |
|
| 691 |
+ |
} |
| 692 |
|
|
| 693 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 694 |
|
|
| 697 |
|
|
| 698 |
|
// scatter/gather pot_row into the members of my column |
| 699 |
|
|
| 700 |
< |
AtomCommPotRow->scatter(pot_row, pot_temp); |
| 700 |
> |
AtomPlanPotRow->scatter(pot_row, pot_temp); |
| 701 |
|
|
| 702 |
|
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 703 |
|
pairwisePot += pot_temp[ii]; |
| 705 |
|
fill(pot_temp.begin(), pot_temp.end(), |
| 706 |
|
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 707 |
|
|
| 708 |
< |
AtomCommPotColumn->scatter(pot_col, pot_temp); |
| 708 |
> |
AtomPlanPotColumn->scatter(pot_col, pot_temp); |
| 709 |
|
|
| 710 |
|
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 711 |
|
pairwisePot += pot_temp[ii]; |
| 712 |
+ |
|
| 713 |
+ |
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
| 714 |
+ |
RealType ploc1 = pairwisePot[ii]; |
| 715 |
+ |
RealType ploc2 = 0.0; |
| 716 |
+ |
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
| 717 |
+ |
pairwisePot[ii] = ploc2; |
| 718 |
+ |
} |
| 719 |
+ |
|
| 720 |
+ |
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
| 721 |
+ |
RealType ploc1 = embeddingPot[ii]; |
| 722 |
+ |
RealType ploc2 = 0.0; |
| 723 |
+ |
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
| 724 |
+ |
embeddingPot[ii] = ploc2; |
| 725 |
+ |
} |
| 726 |
+ |
|
| 727 |
|
#endif |
| 728 |
|
|
| 729 |
|
} |
| 826 |
|
return d; |
| 827 |
|
} |
| 828 |
|
|
| 829 |
< |
vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) { |
| 830 |
< |
return skipsForAtom[atom1]; |
| 829 |
> |
vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) { |
| 830 |
> |
return excludesForAtom[atom1]; |
| 831 |
|
} |
| 832 |
|
|
| 833 |
|
/** |
| 834 |
< |
* There are a number of reasons to skip a pair or a |
| 725 |
< |
* particle. Mostly we do this to exclude atoms who are involved in |
| 726 |
< |
* short range interactions (bonds, bends, torsions), but we also |
| 727 |
< |
* need to exclude some overcounted interactions that result from |
| 834 |
> |
* We need to exclude some overcounted interactions that result from |
| 835 |
|
* the parallel decomposition. |
| 836 |
|
*/ |
| 837 |
|
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 838 |
|
int unique_id_1, unique_id_2; |
| 839 |
< |
|
| 839 |
> |
|
| 840 |
|
#ifdef IS_MPI |
| 841 |
|
// in MPI, we have to look up the unique IDs for each atom |
| 842 |
|
unique_id_1 = AtomRowToGlobal[atom1]; |
| 843 |
|
unique_id_2 = AtomColToGlobal[atom2]; |
| 844 |
+ |
#else |
| 845 |
+ |
unique_id_1 = AtomLocalToGlobal[atom1]; |
| 846 |
+ |
unique_id_2 = AtomLocalToGlobal[atom2]; |
| 847 |
+ |
#endif |
| 848 |
|
|
| 738 |
– |
// this situation should only arise in MPI simulations |
| 849 |
|
if (unique_id_1 == unique_id_2) return true; |
| 850 |
< |
|
| 850 |
> |
|
| 851 |
> |
#ifdef IS_MPI |
| 852 |
|
// this prevents us from doing the pair on multiple processors |
| 853 |
|
if (unique_id_1 < unique_id_2) { |
| 854 |
|
if ((unique_id_1 + unique_id_2) % 2 == 0) return true; |
| 855 |
|
} else { |
| 856 |
< |
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 856 |
> |
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 857 |
|
} |
| 747 |
– |
#else |
| 748 |
– |
// in the normal loop, the atom numbers are unique |
| 749 |
– |
unique_id_1 = atom1; |
| 750 |
– |
unique_id_2 = atom2; |
| 858 |
|
#endif |
| 859 |
|
|
| 860 |
< |
for (vector<int>::iterator i = skipsForAtom[atom1].begin(); |
| 861 |
< |
i != skipsForAtom[atom1].end(); ++i) { |
| 862 |
< |
if ( (*i) == unique_id_2 ) return true; |
| 860 |
> |
return false; |
| 861 |
> |
} |
| 862 |
> |
|
| 863 |
> |
/** |
| 864 |
> |
* We need to handle the interactions for atoms who are involved in |
| 865 |
> |
* the same rigid body as well as some short range interactions |
| 866 |
> |
* (bonds, bends, torsions) differently from other interactions. |
| 867 |
> |
* We'll still visit the pairwise routines, but with a flag that |
| 868 |
> |
* tells those routines to exclude the pair from direct long range |
| 869 |
> |
* interactions. Some indirect interactions (notably reaction |
| 870 |
> |
* field) must still be handled for these pairs. |
| 871 |
> |
*/ |
| 872 |
> |
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
| 873 |
> |
|
| 874 |
> |
// excludesForAtom was constructed to use row/column indices in the MPI |
| 875 |
> |
// version, and to use local IDs in the non-MPI version: |
| 876 |
> |
|
| 877 |
> |
for (vector<int>::iterator i = excludesForAtom[atom1].begin(); |
| 878 |
> |
i != excludesForAtom[atom1].end(); ++i) { |
| 879 |
> |
if ( (*i) == atom2 ) return true; |
| 880 |
|
} |
| 881 |
|
|
| 882 |
|
return false; |
| 901 |
|
|
| 902 |
|
// filling interaction blocks with pointers |
| 903 |
|
void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, |
| 904 |
< |
int atom1, int atom2) { |
| 904 |
> |
int atom1, int atom2) { |
| 905 |
> |
|
| 906 |
> |
idat.excluded = excludeAtomPair(atom1, atom2); |
| 907 |
> |
|
| 908 |
|
#ifdef IS_MPI |
| 909 |
+ |
idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
| 910 |
+ |
//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 911 |
+ |
// ff_->getAtomType(identsCol[atom2]) ); |
| 912 |
|
|
| 783 |
– |
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 784 |
– |
ff_->getAtomType(identsCol[atom2]) ); |
| 785 |
– |
|
| 913 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 914 |
|
idat.A1 = &(atomRowData.aMat[atom1]); |
| 915 |
|
idat.A2 = &(atomColData.aMat[atom2]); |
| 945 |
|
idat.particlePot2 = &(atomColData.particlePot[atom2]); |
| 946 |
|
} |
| 947 |
|
|
| 948 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 949 |
+ |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 950 |
+ |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 951 |
+ |
} |
| 952 |
+ |
|
| 953 |
|
#else |
| 954 |
|
|
| 955 |
< |
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 956 |
< |
ff_->getAtomType(idents[atom2]) ); |
| 955 |
> |
idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
| 956 |
> |
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 957 |
> |
// ff_->getAtomType(idents[atom2]) ); |
| 958 |
|
|
| 959 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 960 |
|
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 991 |
|
idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
| 992 |
|
} |
| 993 |
|
|
| 994 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 995 |
+ |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 996 |
+ |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 997 |
+ |
} |
| 998 |
|
#endif |
| 999 |
|
} |
| 1000 |
|
|
| 1001 |
|
|
| 1002 |
|
void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
| 1003 |
|
#ifdef IS_MPI |
| 1004 |
< |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 1005 |
< |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 1004 |
> |
pot_row[atom1] += RealType(0.5) * *(idat.pot); |
| 1005 |
> |
pot_col[atom2] += RealType(0.5) * *(idat.pot); |
| 1006 |
|
|
| 1007 |
|
atomRowData.force[atom1] += *(idat.f1); |
| 1008 |
|
atomColData.force[atom2] -= *(idat.f1); |
| 1012 |
|
snap_->atomData.force[atom1] += *(idat.f1); |
| 1013 |
|
snap_->atomData.force[atom2] -= *(idat.f1); |
| 1014 |
|
#endif |
| 1015 |
< |
|
| 1015 |
> |
|
| 1016 |
|
} |
| 1017 |
|
|
| 881 |
– |
|
| 882 |
– |
void ForceMatrixDecomposition::fillSkipData(InteractionData &idat, |
| 883 |
– |
int atom1, int atom2) { |
| 884 |
– |
// Still Missing:: skippedCharge fill must be added to DataStorage |
| 885 |
– |
#ifdef IS_MPI |
| 886 |
– |
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 887 |
– |
ff_->getAtomType(identsCol[atom2]) ); |
| 888 |
– |
|
| 889 |
– |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 890 |
– |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 891 |
– |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 892 |
– |
} |
| 893 |
– |
if (storageLayout_ & DataStorage::dslTorque) { |
| 894 |
– |
idat.t1 = &(atomRowData.torque[atom1]); |
| 895 |
– |
idat.t2 = &(atomColData.torque[atom2]); |
| 896 |
– |
} |
| 897 |
– |
#else |
| 898 |
– |
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 899 |
– |
ff_->getAtomType(idents[atom2]) ); |
| 900 |
– |
|
| 901 |
– |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 902 |
– |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 903 |
– |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 904 |
– |
} |
| 905 |
– |
if (storageLayout_ & DataStorage::dslTorque) { |
| 906 |
– |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 907 |
– |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 908 |
– |
} |
| 909 |
– |
#endif |
| 910 |
– |
} |
| 911 |
– |
|
| 912 |
– |
|
| 913 |
– |
void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) { |
| 914 |
– |
#ifdef IS_MPI |
| 915 |
– |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 916 |
– |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 917 |
– |
#else |
| 918 |
– |
pairwisePot += *(idat.pot); |
| 919 |
– |
#endif |
| 920 |
– |
|
| 921 |
– |
} |
| 922 |
– |
|
| 923 |
– |
|
| 1018 |
|
/* |
| 1019 |
|
* buildNeighborList |
| 1020 |
|
* |
| 1025 |
|
|
| 1026 |
|
vector<pair<int, int> > neighborList; |
| 1027 |
|
groupCutoffs cuts; |
| 1028 |
+ |
bool doAllPairs = false; |
| 1029 |
+ |
|
| 1030 |
|
#ifdef IS_MPI |
| 1031 |
|
cellListRow_.clear(); |
| 1032 |
|
cellListCol_.clear(); |
| 1046 |
|
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 1047 |
|
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 1048 |
|
|
| 1049 |
+ |
// handle small boxes where the cell offsets can end up repeating cells |
| 1050 |
+ |
|
| 1051 |
+ |
if (nCells_.x() < 3) doAllPairs = true; |
| 1052 |
+ |
if (nCells_.y() < 3) doAllPairs = true; |
| 1053 |
+ |
if (nCells_.z() < 3) doAllPairs = true; |
| 1054 |
+ |
|
| 1055 |
|
Mat3x3d invHmat = snap_->getInvHmat(); |
| 1056 |
|
Vector3d rs, scaled, dr; |
| 1057 |
|
Vector3i whichCell; |
| 1065 |
|
cellList_.resize(nCtot); |
| 1066 |
|
#endif |
| 1067 |
|
|
| 1068 |
+ |
if (!doAllPairs) { |
| 1069 |
|
#ifdef IS_MPI |
| 967 |
– |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 968 |
– |
rs = cgRowData.position[i]; |
| 969 |
– |
|
| 970 |
– |
// scaled positions relative to the box vectors |
| 971 |
– |
scaled = invHmat * rs; |
| 1070 |
|
|
| 1071 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 1072 |
< |
// numbers |
| 1073 |
< |
for (int j = 0; j < 3; j++) { |
| 1074 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 1075 |
< |
scaled[j] += 0.5; |
| 1071 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 1072 |
> |
rs = cgRowData.position[i]; |
| 1073 |
> |
|
| 1074 |
> |
// scaled positions relative to the box vectors |
| 1075 |
> |
scaled = invHmat * rs; |
| 1076 |
> |
|
| 1077 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1078 |
> |
// numbers |
| 1079 |
> |
for (int j = 0; j < 3; j++) { |
| 1080 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1081 |
> |
scaled[j] += 0.5; |
| 1082 |
> |
} |
| 1083 |
> |
|
| 1084 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1085 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1086 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1087 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1088 |
> |
|
| 1089 |
> |
// find single index of this cell: |
| 1090 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1091 |
> |
|
| 1092 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1093 |
> |
cellListRow_[cellIndex].push_back(i); |
| 1094 |
|
} |
| 1095 |
< |
|
| 1096 |
< |
// find xyz-indices of cell that cutoffGroup is in. |
| 1097 |
< |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1098 |
< |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1099 |
< |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1100 |
< |
|
| 1101 |
< |
// find single index of this cell: |
| 1102 |
< |
cellIndex = Vlinear(whichCell, nCells_); |
| 1103 |
< |
|
| 1104 |
< |
// add this cutoff group to the list of groups in this cell; |
| 1105 |
< |
cellListRow_[cellIndex].push_back(i); |
| 1106 |
< |
} |
| 1107 |
< |
|
| 1108 |
< |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 1109 |
< |
rs = cgColData.position[i]; |
| 1110 |
< |
|
| 1111 |
< |
// scaled positions relative to the box vectors |
| 1112 |
< |
scaled = invHmat * rs; |
| 1113 |
< |
|
| 1114 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 1115 |
< |
// numbers |
| 1116 |
< |
for (int j = 0; j < 3; j++) { |
| 1117 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 1002 |
< |
scaled[j] += 0.5; |
| 1095 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 1096 |
> |
rs = cgColData.position[i]; |
| 1097 |
> |
|
| 1098 |
> |
// scaled positions relative to the box vectors |
| 1099 |
> |
scaled = invHmat * rs; |
| 1100 |
> |
|
| 1101 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1102 |
> |
// numbers |
| 1103 |
> |
for (int j = 0; j < 3; j++) { |
| 1104 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1105 |
> |
scaled[j] += 0.5; |
| 1106 |
> |
} |
| 1107 |
> |
|
| 1108 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1109 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1110 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1111 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1112 |
> |
|
| 1113 |
> |
// find single index of this cell: |
| 1114 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1115 |
> |
|
| 1116 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1117 |
> |
cellListCol_[cellIndex].push_back(i); |
| 1118 |
|
} |
| 1119 |
< |
|
| 1005 |
< |
// find xyz-indices of cell that cutoffGroup is in. |
| 1006 |
< |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1007 |
< |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1008 |
< |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1009 |
< |
|
| 1010 |
< |
// find single index of this cell: |
| 1011 |
< |
cellIndex = Vlinear(whichCell, nCells_); |
| 1012 |
< |
|
| 1013 |
< |
// add this cutoff group to the list of groups in this cell; |
| 1014 |
< |
cellListCol_[cellIndex].push_back(i); |
| 1015 |
< |
} |
| 1119 |
> |
|
| 1120 |
|
#else |
| 1121 |
< |
for (int i = 0; i < nGroups_; i++) { |
| 1122 |
< |
rs = snap_->cgData.position[i]; |
| 1123 |
< |
|
| 1124 |
< |
// scaled positions relative to the box vectors |
| 1125 |
< |
scaled = invHmat * rs; |
| 1126 |
< |
|
| 1127 |
< |
// wrap the vector back into the unit box by subtracting integer box |
| 1128 |
< |
// numbers |
| 1129 |
< |
for (int j = 0; j < 3; j++) { |
| 1130 |
< |
scaled[j] -= roundMe(scaled[j]); |
| 1131 |
< |
scaled[j] += 0.5; |
| 1121 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 1122 |
> |
rs = snap_->cgData.position[i]; |
| 1123 |
> |
|
| 1124 |
> |
// scaled positions relative to the box vectors |
| 1125 |
> |
scaled = invHmat * rs; |
| 1126 |
> |
|
| 1127 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1128 |
> |
// numbers |
| 1129 |
> |
for (int j = 0; j < 3; j++) { |
| 1130 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1131 |
> |
scaled[j] += 0.5; |
| 1132 |
> |
} |
| 1133 |
> |
|
| 1134 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1135 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1136 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1137 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1138 |
> |
|
| 1139 |
> |
// find single index of this cell: |
| 1140 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1141 |
> |
|
| 1142 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1143 |
> |
cellList_[cellIndex].push_back(i); |
| 1144 |
|
} |
| 1145 |
|
|
| 1030 |
– |
// find xyz-indices of cell that cutoffGroup is in. |
| 1031 |
– |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1032 |
– |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1033 |
– |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1034 |
– |
|
| 1035 |
– |
// find single index of this cell: |
| 1036 |
– |
cellIndex = Vlinear(whichCell, nCells_); |
| 1037 |
– |
|
| 1038 |
– |
// add this cutoff group to the list of groups in this cell; |
| 1039 |
– |
cellList_[cellIndex].push_back(i); |
| 1040 |
– |
} |
| 1146 |
|
#endif |
| 1147 |
|
|
| 1148 |
< |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 1149 |
< |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 1150 |
< |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 1151 |
< |
Vector3i m1v(m1x, m1y, m1z); |
| 1152 |
< |
int m1 = Vlinear(m1v, nCells_); |
| 1048 |
< |
|
| 1049 |
< |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 1050 |
< |
os != cellOffsets_.end(); ++os) { |
| 1148 |
> |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 1149 |
> |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 1150 |
> |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 1151 |
> |
Vector3i m1v(m1x, m1y, m1z); |
| 1152 |
> |
int m1 = Vlinear(m1v, nCells_); |
| 1153 |
|
|
| 1154 |
< |
Vector3i m2v = m1v + (*os); |
| 1155 |
< |
|
| 1156 |
< |
if (m2v.x() >= nCells_.x()) { |
| 1157 |
< |
m2v.x() = 0; |
| 1158 |
< |
} else if (m2v.x() < 0) { |
| 1057 |
< |
m2v.x() = nCells_.x() - 1; |
| 1058 |
< |
} |
| 1059 |
< |
|
| 1060 |
< |
if (m2v.y() >= nCells_.y()) { |
| 1061 |
< |
m2v.y() = 0; |
| 1062 |
< |
} else if (m2v.y() < 0) { |
| 1063 |
< |
m2v.y() = nCells_.y() - 1; |
| 1064 |
< |
} |
| 1065 |
< |
|
| 1066 |
< |
if (m2v.z() >= nCells_.z()) { |
| 1067 |
< |
m2v.z() = 0; |
| 1068 |
< |
} else if (m2v.z() < 0) { |
| 1069 |
< |
m2v.z() = nCells_.z() - 1; |
| 1070 |
< |
} |
| 1071 |
< |
|
| 1072 |
< |
int m2 = Vlinear (m2v, nCells_); |
| 1154 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 1155 |
> |
os != cellOffsets_.end(); ++os) { |
| 1156 |
> |
|
| 1157 |
> |
Vector3i m2v = m1v + (*os); |
| 1158 |
> |
|
| 1159 |
|
|
| 1160 |
< |
#ifdef IS_MPI |
| 1161 |
< |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1162 |
< |
j1 != cellListRow_[m1].end(); ++j1) { |
| 1163 |
< |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1164 |
< |
j2 != cellListCol_[m2].end(); ++j2) { |
| 1165 |
< |
|
| 1166 |
< |
// Always do this if we're in different cells or if |
| 1167 |
< |
// we're in the same cell and the global index of the |
| 1168 |
< |
// j2 cutoff group is less than the j1 cutoff group |
| 1160 |
> |
if (m2v.x() >= nCells_.x()) { |
| 1161 |
> |
m2v.x() = 0; |
| 1162 |
> |
} else if (m2v.x() < 0) { |
| 1163 |
> |
m2v.x() = nCells_.x() - 1; |
| 1164 |
> |
} |
| 1165 |
> |
|
| 1166 |
> |
if (m2v.y() >= nCells_.y()) { |
| 1167 |
> |
m2v.y() = 0; |
| 1168 |
> |
} else if (m2v.y() < 0) { |
| 1169 |
> |
m2v.y() = nCells_.y() - 1; |
| 1170 |
> |
} |
| 1171 |
> |
|
| 1172 |
> |
if (m2v.z() >= nCells_.z()) { |
| 1173 |
> |
m2v.z() = 0; |
| 1174 |
> |
} else if (m2v.z() < 0) { |
| 1175 |
> |
m2v.z() = nCells_.z() - 1; |
| 1176 |
> |
} |
| 1177 |
|
|
| 1178 |
< |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 1178 |
> |
int m2 = Vlinear (m2v, nCells_); |
| 1179 |
> |
|
| 1180 |
> |
#ifdef IS_MPI |
| 1181 |
> |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1182 |
> |
j1 != cellListRow_[m1].end(); ++j1) { |
| 1183 |
> |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1184 |
> |
j2 != cellListCol_[m2].end(); ++j2) { |
| 1185 |
> |
|
| 1186 |
> |
// In parallel, we need to visit *all* pairs of row |
| 1187 |
> |
// & column indicies and will divide labor in the |
| 1188 |
> |
// force evaluation later. |
| 1189 |
|
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 1190 |
|
snap_->wrapVector(dr); |
| 1191 |
|
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1192 |
|
if (dr.lengthSquare() < cuts.third) { |
| 1193 |
|
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1194 |
< |
} |
| 1194 |
> |
} |
| 1195 |
|
} |
| 1196 |
|
} |
| 1093 |
– |
} |
| 1197 |
|
#else |
| 1198 |
+ |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 1199 |
+ |
j1 != cellList_[m1].end(); ++j1) { |
| 1200 |
+ |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 1201 |
+ |
j2 != cellList_[m2].end(); ++j2) { |
| 1202 |
+ |
|
| 1203 |
+ |
// Always do this if we're in different cells or if |
| 1204 |
+ |
// we're in the same cell and the global index of |
| 1205 |
+ |
// the j2 cutoff group is greater than or equal to |
| 1206 |
+ |
// the j1 cutoff group. Note that Rappaport's code |
| 1207 |
+ |
// has a "less than" conditional here, but that |
| 1208 |
+ |
// deals with atom-by-atom computation. OpenMD |
| 1209 |
+ |
// allows atoms within a single cutoff group to |
| 1210 |
+ |
// interact with each other. |
| 1211 |
|
|
| 1096 |
– |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 1097 |
– |
j1 != cellList_[m1].end(); ++j1) { |
| 1098 |
– |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 1099 |
– |
j2 != cellList_[m2].end(); ++j2) { |
| 1212 |
|
|
| 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 |
| 1213 |
|
|
| 1214 |
< |
if (m2 != m1 || (*j2) < (*j1)) { |
| 1215 |
< |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1216 |
< |
snap_->wrapVector(dr); |
| 1217 |
< |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1218 |
< |
if (dr.lengthSquare() < cuts.third) { |
| 1219 |
< |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1214 |
> |
if (m2 != m1 || (*j2) >= (*j1) ) { |
| 1215 |
> |
|
| 1216 |
> |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1217 |
> |
snap_->wrapVector(dr); |
| 1218 |
> |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1219 |
> |
if (dr.lengthSquare() < cuts.third) { |
| 1220 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1221 |
> |
} |
| 1222 |
|
} |
| 1223 |
|
} |
| 1224 |
|
} |
| 1114 |
– |
} |
| 1225 |
|
#endif |
| 1226 |
+ |
} |
| 1227 |
|
} |
| 1228 |
|
} |
| 1229 |
|
} |
| 1230 |
+ |
} else { |
| 1231 |
+ |
// branch to do all cutoff group pairs |
| 1232 |
+ |
#ifdef IS_MPI |
| 1233 |
+ |
for (int j1 = 0; j1 < nGroupsInRow_; j1++) { |
| 1234 |
+ |
for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
| 1235 |
+ |
dr = cgColData.position[j2] - cgRowData.position[j1]; |
| 1236 |
+ |
snap_->wrapVector(dr); |
| 1237 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1238 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1239 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1240 |
+ |
} |
| 1241 |
+ |
} |
| 1242 |
+ |
} |
| 1243 |
+ |
#else |
| 1244 |
+ |
// include all groups here. |
| 1245 |
+ |
for (int j1 = 0; j1 < nGroups_; j1++) { |
| 1246 |
+ |
// include self group interactions j2 == j1 |
| 1247 |
+ |
for (int j2 = j1; j2 < nGroups_; j2++) { |
| 1248 |
+ |
dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; |
| 1249 |
+ |
snap_->wrapVector(dr); |
| 1250 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1251 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1252 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1253 |
+ |
} |
| 1254 |
+ |
} |
| 1255 |
+ |
} |
| 1256 |
+ |
#endif |
| 1257 |
|
} |
| 1258 |
< |
|
| 1258 |
> |
|
| 1259 |
|
// save the local cutoff group positions for the check that is |
| 1260 |
|
// done on each loop: |
| 1261 |
|
saved_CG_positions_.clear(); |
| 1262 |
|
for (int i = 0; i < nGroups_; i++) |
| 1263 |
|
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 1264 |
< |
|
| 1264 |
> |
|
| 1265 |
|
return neighborList; |
| 1266 |
|
} |
| 1267 |
|
} //end namespace OpenMD |
