| 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 { |
| 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 |
|
|
| 99 |
– |
// gather the information for atomtype IDs (atids): |
| 100 |
– |
vector<int> identsLocal = info_->getIdentArray(); |
| 101 |
– |
identsRow.reserve(nAtomsInRow); |
| 102 |
– |
identsCol.reserve(nAtomsInCol); |
| 103 |
– |
|
| 104 |
– |
AtomCommIntRow->gather(identsLocal, identsRow); |
| 105 |
– |
AtomCommIntColumn->gather(identsLocal, identsCol); |
| 106 |
– |
|
| 107 |
– |
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 115 |
|
AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 116 |
|
AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 117 |
|
|
| 111 |
– |
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 118 |
|
cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 119 |
|
cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 120 |
|
|
| 121 |
< |
// still need: |
| 122 |
< |
// topoDist |
| 123 |
< |
// exclude |
| 121 |
> |
AtomCommRealRow->gather(massFactors, massFactorsRow); |
| 122 |
> |
AtomCommRealColumn->gather(massFactors, massFactorsCol); |
| 123 |
> |
|
| 124 |
> |
groupListRow_.clear(); |
| 125 |
> |
groupListRow_.resize(nGroupsInRow_); |
| 126 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 127 |
> |
int gid = cgRowToGlobal[i]; |
| 128 |
> |
for (int j = 0; j < nAtomsInRow_; j++) { |
| 129 |
> |
int aid = AtomRowToGlobal[j]; |
| 130 |
> |
if (globalGroupMembership[aid] == gid) |
| 131 |
> |
groupListRow_[i].push_back(j); |
| 132 |
> |
} |
| 133 |
> |
} |
| 134 |
> |
|
| 135 |
> |
groupListCol_.clear(); |
| 136 |
> |
groupListCol_.resize(nGroupsInCol_); |
| 137 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 138 |
> |
int gid = cgColToGlobal[i]; |
| 139 |
> |
for (int j = 0; j < nAtomsInCol_; j++) { |
| 140 |
> |
int aid = AtomColToGlobal[j]; |
| 141 |
> |
if (globalGroupMembership[aid] == gid) |
| 142 |
> |
groupListCol_[i].push_back(j); |
| 143 |
> |
} |
| 144 |
> |
} |
| 145 |
> |
|
| 146 |
> |
excludesForAtom.clear(); |
| 147 |
> |
excludesForAtom.resize(nAtomsInRow_); |
| 148 |
> |
toposForAtom.clear(); |
| 149 |
> |
toposForAtom.resize(nAtomsInRow_); |
| 150 |
> |
topoDist.clear(); |
| 151 |
> |
topoDist.resize(nAtomsInRow_); |
| 152 |
> |
for (int i = 0; i < nAtomsInRow_; i++) { |
| 153 |
> |
int iglob = AtomRowToGlobal[i]; |
| 154 |
> |
|
| 155 |
> |
for (int j = 0; j < nAtomsInCol_; j++) { |
| 156 |
> |
int jglob = AtomColToGlobal[j]; |
| 157 |
> |
|
| 158 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 159 |
> |
excludesForAtom[i].push_back(j); |
| 160 |
> |
|
| 161 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 162 |
> |
toposForAtom[i].push_back(j); |
| 163 |
> |
topoDist[i].push_back(1); |
| 164 |
> |
} else { |
| 165 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 166 |
> |
toposForAtom[i].push_back(j); |
| 167 |
> |
topoDist[i].push_back(2); |
| 168 |
> |
} else { |
| 169 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 170 |
> |
toposForAtom[i].push_back(j); |
| 171 |
> |
topoDist[i].push_back(3); |
| 172 |
> |
} |
| 173 |
> |
} |
| 174 |
> |
} |
| 175 |
> |
} |
| 176 |
> |
} |
| 177 |
> |
|
| 178 |
> |
#endif |
| 179 |
> |
|
| 180 |
> |
groupList_.clear(); |
| 181 |
> |
groupList_.resize(nGroups_); |
| 182 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 183 |
> |
int gid = cgLocalToGlobal[i]; |
| 184 |
> |
for (int j = 0; j < nLocal_; j++) { |
| 185 |
> |
int aid = AtomLocalToGlobal[j]; |
| 186 |
> |
if (globalGroupMembership[aid] == gid) { |
| 187 |
> |
groupList_[i].push_back(j); |
| 188 |
> |
} |
| 189 |
> |
} |
| 190 |
> |
} |
| 191 |
> |
|
| 192 |
> |
excludesForAtom.clear(); |
| 193 |
> |
excludesForAtom.resize(nLocal_); |
| 194 |
> |
toposForAtom.clear(); |
| 195 |
> |
toposForAtom.resize(nLocal_); |
| 196 |
> |
topoDist.clear(); |
| 197 |
> |
topoDist.resize(nLocal_); |
| 198 |
> |
|
| 199 |
> |
for (int i = 0; i < nLocal_; i++) { |
| 200 |
> |
int iglob = AtomLocalToGlobal[i]; |
| 201 |
> |
|
| 202 |
> |
for (int j = 0; j < nLocal_; j++) { |
| 203 |
> |
int jglob = AtomLocalToGlobal[j]; |
| 204 |
> |
|
| 205 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 206 |
> |
excludesForAtom[i].push_back(j); |
| 207 |
> |
|
| 208 |
> |
if (oneTwo->hasPair(iglob, jglob)) { |
| 209 |
> |
toposForAtom[i].push_back(j); |
| 210 |
> |
topoDist[i].push_back(1); |
| 211 |
> |
} else { |
| 212 |
> |
if (oneThree->hasPair(iglob, jglob)) { |
| 213 |
> |
toposForAtom[i].push_back(j); |
| 214 |
> |
topoDist[i].push_back(2); |
| 215 |
> |
} else { |
| 216 |
> |
if (oneFour->hasPair(iglob, jglob)) { |
| 217 |
> |
toposForAtom[i].push_back(j); |
| 218 |
> |
topoDist[i].push_back(3); |
| 219 |
> |
} |
| 220 |
> |
} |
| 221 |
> |
} |
| 222 |
> |
} |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
createGtypeCutoffMap(); |
| 226 |
> |
|
| 227 |
> |
} |
| 228 |
> |
|
| 229 |
> |
void ForceMatrixDecomposition::createGtypeCutoffMap() { |
| 230 |
> |
|
| 231 |
> |
RealType tol = 1e-6; |
| 232 |
> |
RealType rc; |
| 233 |
> |
int atid; |
| 234 |
> |
set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
| 235 |
> |
map<int, RealType> atypeCutoff; |
| 236 |
> |
|
| 237 |
> |
for (set<AtomType*>::iterator at = atypes.begin(); |
| 238 |
> |
at != atypes.end(); ++at){ |
| 239 |
> |
atid = (*at)->getIdent(); |
| 240 |
> |
if (userChoseCutoff_) |
| 241 |
> |
atypeCutoff[atid] = userCutoff_; |
| 242 |
> |
else |
| 243 |
> |
atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
| 244 |
> |
} |
| 245 |
> |
|
| 246 |
> |
vector<RealType> gTypeCutoffs; |
| 247 |
> |
// first we do a single loop over the cutoff groups to find the |
| 248 |
> |
// largest cutoff for any atypes present in this group. |
| 249 |
> |
#ifdef IS_MPI |
| 250 |
> |
vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0); |
| 251 |
> |
groupRowToGtype.resize(nGroupsInRow_); |
| 252 |
> |
for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) { |
| 253 |
> |
vector<int> atomListRow = getAtomsInGroupRow(cg1); |
| 254 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 255 |
> |
ia != atomListRow.end(); ++ia) { |
| 256 |
> |
int atom1 = (*ia); |
| 257 |
> |
atid = identsRow[atom1]; |
| 258 |
> |
if (atypeCutoff[atid] > groupCutoffRow[cg1]) { |
| 259 |
> |
groupCutoffRow[cg1] = atypeCutoff[atid]; |
| 260 |
> |
} |
| 261 |
> |
} |
| 262 |
> |
|
| 263 |
> |
bool gTypeFound = false; |
| 264 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
| 265 |
> |
if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) { |
| 266 |
> |
groupRowToGtype[cg1] = gt; |
| 267 |
> |
gTypeFound = true; |
| 268 |
> |
} |
| 269 |
> |
} |
| 270 |
> |
if (!gTypeFound) { |
| 271 |
> |
gTypeCutoffs.push_back( groupCutoffRow[cg1] ); |
| 272 |
> |
groupRowToGtype[cg1] = gTypeCutoffs.size() - 1; |
| 273 |
> |
} |
| 274 |
> |
|
| 275 |
> |
} |
| 276 |
> |
vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0); |
| 277 |
> |
groupColToGtype.resize(nGroupsInCol_); |
| 278 |
> |
for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) { |
| 279 |
> |
vector<int> atomListCol = getAtomsInGroupColumn(cg2); |
| 280 |
> |
for (vector<int>::iterator jb = atomListCol.begin(); |
| 281 |
> |
jb != atomListCol.end(); ++jb) { |
| 282 |
> |
int atom2 = (*jb); |
| 283 |
> |
atid = identsCol[atom2]; |
| 284 |
> |
if (atypeCutoff[atid] > groupCutoffCol[cg2]) { |
| 285 |
> |
groupCutoffCol[cg2] = atypeCutoff[atid]; |
| 286 |
> |
} |
| 287 |
> |
} |
| 288 |
> |
bool gTypeFound = false; |
| 289 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
| 290 |
> |
if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) { |
| 291 |
> |
groupColToGtype[cg2] = gt; |
| 292 |
> |
gTypeFound = true; |
| 293 |
> |
} |
| 294 |
> |
} |
| 295 |
> |
if (!gTypeFound) { |
| 296 |
> |
gTypeCutoffs.push_back( groupCutoffCol[cg2] ); |
| 297 |
> |
groupColToGtype[cg2] = gTypeCutoffs.size() - 1; |
| 298 |
> |
} |
| 299 |
> |
} |
| 300 |
> |
#else |
| 301 |
> |
|
| 302 |
> |
vector<RealType> groupCutoff(nGroups_, 0.0); |
| 303 |
> |
groupToGtype.resize(nGroups_); |
| 304 |
> |
for (int cg1 = 0; cg1 < nGroups_; cg1++) { |
| 305 |
> |
|
| 306 |
> |
groupCutoff[cg1] = 0.0; |
| 307 |
> |
vector<int> atomList = getAtomsInGroupRow(cg1); |
| 308 |
> |
|
| 309 |
> |
for (vector<int>::iterator ia = atomList.begin(); |
| 310 |
> |
ia != atomList.end(); ++ia) { |
| 311 |
> |
int atom1 = (*ia); |
| 312 |
> |
atid = idents[atom1]; |
| 313 |
> |
if (atypeCutoff[atid] > groupCutoff[cg1]) { |
| 314 |
> |
groupCutoff[cg1] = atypeCutoff[atid]; |
| 315 |
> |
} |
| 316 |
> |
} |
| 317 |
> |
|
| 318 |
> |
bool gTypeFound = false; |
| 319 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { |
| 320 |
> |
if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) { |
| 321 |
> |
groupToGtype[cg1] = gt; |
| 322 |
> |
gTypeFound = true; |
| 323 |
> |
} |
| 324 |
> |
} |
| 325 |
> |
if (!gTypeFound) { |
| 326 |
> |
gTypeCutoffs.push_back( groupCutoff[cg1] ); |
| 327 |
> |
groupToGtype[cg1] = gTypeCutoffs.size() - 1; |
| 328 |
> |
} |
| 329 |
> |
} |
| 330 |
|
#endif |
| 331 |
+ |
|
| 332 |
+ |
// Now we find the maximum group cutoff value present in the simulation |
| 333 |
+ |
|
| 334 |
+ |
RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
| 335 |
+ |
|
| 336 |
+ |
#ifdef IS_MPI |
| 337 |
+ |
MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX); |
| 338 |
+ |
#endif |
| 339 |
+ |
|
| 340 |
+ |
RealType tradRcut = groupMax; |
| 341 |
+ |
|
| 342 |
+ |
for (int i = 0; i < gTypeCutoffs.size(); i++) { |
| 343 |
+ |
for (int j = 0; j < gTypeCutoffs.size(); j++) { |
| 344 |
+ |
RealType thisRcut; |
| 345 |
+ |
switch(cutoffPolicy_) { |
| 346 |
+ |
case TRADITIONAL: |
| 347 |
+ |
thisRcut = tradRcut; |
| 348 |
+ |
break; |
| 349 |
+ |
case MIX: |
| 350 |
+ |
thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]); |
| 351 |
+ |
break; |
| 352 |
+ |
case MAX: |
| 353 |
+ |
thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]); |
| 354 |
+ |
break; |
| 355 |
+ |
default: |
| 356 |
+ |
sprintf(painCave.errMsg, |
| 357 |
+ |
"ForceMatrixDecomposition::createGtypeCutoffMap " |
| 358 |
+ |
"hit an unknown cutoff policy!\n"); |
| 359 |
+ |
painCave.severity = OPENMD_ERROR; |
| 360 |
+ |
painCave.isFatal = 1; |
| 361 |
+ |
simError(); |
| 362 |
+ |
break; |
| 363 |
+ |
} |
| 364 |
+ |
|
| 365 |
+ |
pair<int,int> key = make_pair(i,j); |
| 366 |
+ |
gTypeCutoffMap[key].first = thisRcut; |
| 367 |
+ |
|
| 368 |
+ |
if (thisRcut > largestRcut_) largestRcut_ = thisRcut; |
| 369 |
+ |
|
| 370 |
+ |
gTypeCutoffMap[key].second = thisRcut*thisRcut; |
| 371 |
+ |
|
| 372 |
+ |
gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); |
| 373 |
+ |
|
| 374 |
+ |
// sanity check |
| 375 |
+ |
|
| 376 |
+ |
if (userChoseCutoff_) { |
| 377 |
+ |
if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) { |
| 378 |
+ |
sprintf(painCave.errMsg, |
| 379 |
+ |
"ForceMatrixDecomposition::createGtypeCutoffMap " |
| 380 |
+ |
"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_); |
| 381 |
+ |
painCave.severity = OPENMD_ERROR; |
| 382 |
+ |
painCave.isFatal = 1; |
| 383 |
+ |
simError(); |
| 384 |
+ |
} |
| 385 |
+ |
} |
| 386 |
+ |
} |
| 387 |
+ |
} |
| 388 |
|
} |
| 389 |
+ |
|
| 390 |
+ |
|
| 391 |
+ |
groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) { |
| 392 |
+ |
int i, j; |
| 393 |
+ |
#ifdef IS_MPI |
| 394 |
+ |
i = groupRowToGtype[cg1]; |
| 395 |
+ |
j = groupColToGtype[cg2]; |
| 396 |
+ |
#else |
| 397 |
+ |
i = groupToGtype[cg1]; |
| 398 |
+ |
j = groupToGtype[cg2]; |
| 399 |
+ |
#endif |
| 400 |
+ |
return gTypeCutoffMap[make_pair(i,j)]; |
| 401 |
+ |
} |
| 402 |
+ |
|
| 403 |
+ |
int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) { |
| 404 |
+ |
for (int j = 0; j < toposForAtom[atom1].size(); j++) { |
| 405 |
+ |
if (toposForAtom[atom1][j] == atom2) |
| 406 |
+ |
return topoDist[atom1][j]; |
| 407 |
+ |
} |
| 408 |
+ |
return 0; |
| 409 |
+ |
} |
| 410 |
+ |
|
| 411 |
+ |
void ForceMatrixDecomposition::zeroWorkArrays() { |
| 412 |
+ |
pairwisePot = 0.0; |
| 413 |
+ |
embeddingPot = 0.0; |
| 414 |
+ |
|
| 415 |
+ |
#ifdef IS_MPI |
| 416 |
+ |
if (storageLayout_ & DataStorage::dslForce) { |
| 417 |
+ |
fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero); |
| 418 |
+ |
fill(atomColData.force.begin(), atomColData.force.end(), V3Zero); |
| 419 |
+ |
} |
| 420 |
+ |
|
| 421 |
+ |
if (storageLayout_ & DataStorage::dslTorque) { |
| 422 |
+ |
fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero); |
| 423 |
+ |
fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero); |
| 424 |
+ |
} |
| 425 |
|
|
| 426 |
+ |
fill(pot_row.begin(), pot_row.end(), |
| 427 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 428 |
|
|
| 429 |
+ |
fill(pot_col.begin(), pot_col.end(), |
| 430 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 431 |
|
|
| 432 |
+ |
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 433 |
+ |
fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0); |
| 434 |
+ |
fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0); |
| 435 |
+ |
} |
| 436 |
+ |
|
| 437 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 438 |
+ |
fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0); |
| 439 |
+ |
fill(atomColData.density.begin(), atomColData.density.end(), 0.0); |
| 440 |
+ |
} |
| 441 |
+ |
|
| 442 |
+ |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 443 |
+ |
fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0); |
| 444 |
+ |
fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0); |
| 445 |
+ |
} |
| 446 |
+ |
|
| 447 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 448 |
+ |
fill(atomRowData.functionalDerivative.begin(), |
| 449 |
+ |
atomRowData.functionalDerivative.end(), 0.0); |
| 450 |
+ |
fill(atomColData.functionalDerivative.begin(), |
| 451 |
+ |
atomColData.functionalDerivative.end(), 0.0); |
| 452 |
+ |
} |
| 453 |
+ |
|
| 454 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 455 |
+ |
fill(atomRowData.skippedCharge.begin(), |
| 456 |
+ |
atomRowData.skippedCharge.end(), 0.0); |
| 457 |
+ |
fill(atomColData.skippedCharge.begin(), |
| 458 |
+ |
atomColData.skippedCharge.end(), 0.0); |
| 459 |
+ |
} |
| 460 |
+ |
|
| 461 |
+ |
#else |
| 462 |
+ |
|
| 463 |
+ |
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 464 |
+ |
fill(snap_->atomData.particlePot.begin(), |
| 465 |
+ |
snap_->atomData.particlePot.end(), 0.0); |
| 466 |
+ |
} |
| 467 |
+ |
|
| 468 |
+ |
if (storageLayout_ & DataStorage::dslDensity) { |
| 469 |
+ |
fill(snap_->atomData.density.begin(), |
| 470 |
+ |
snap_->atomData.density.end(), 0.0); |
| 471 |
+ |
} |
| 472 |
+ |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 473 |
+ |
fill(snap_->atomData.functional.begin(), |
| 474 |
+ |
snap_->atomData.functional.end(), 0.0); |
| 475 |
+ |
} |
| 476 |
+ |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 477 |
+ |
fill(snap_->atomData.functionalDerivative.begin(), |
| 478 |
+ |
snap_->atomData.functionalDerivative.end(), 0.0); |
| 479 |
+ |
} |
| 480 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 481 |
+ |
fill(snap_->atomData.skippedCharge.begin(), |
| 482 |
+ |
snap_->atomData.skippedCharge.end(), 0.0); |
| 483 |
+ |
} |
| 484 |
+ |
#endif |
| 485 |
+ |
|
| 486 |
+ |
} |
| 487 |
+ |
|
| 488 |
+ |
|
| 489 |
|
void ForceMatrixDecomposition::distributeData() { |
| 490 |
|
snap_ = sman_->getCurrentSnapshot(); |
| 491 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 521 |
|
#endif |
| 522 |
|
} |
| 523 |
|
|
| 524 |
+ |
/* collects information obtained during the pre-pair loop onto local |
| 525 |
+ |
* data structures. |
| 526 |
+ |
*/ |
| 527 |
|
void ForceMatrixDecomposition::collectIntermediateData() { |
| 528 |
|
snap_ = sman_->getCurrentSnapshot(); |
| 529 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 535 |
|
snap_->atomData.density); |
| 536 |
|
|
| 537 |
|
int n = snap_->atomData.density.size(); |
| 538 |
< |
std::vector<RealType> rho_tmp(n, 0.0); |
| 538 |
> |
vector<RealType> rho_tmp(n, 0.0); |
| 539 |
|
AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
| 540 |
|
for (int i = 0; i < n; i++) |
| 541 |
|
snap_->atomData.density[i] += rho_tmp[i]; |
| 542 |
|
} |
| 543 |
|
#endif |
| 544 |
|
} |
| 545 |
< |
|
| 545 |
> |
|
| 546 |
> |
/* |
| 547 |
> |
* redistributes information obtained during the pre-pair loop out to |
| 548 |
> |
* row and column-indexed data structures |
| 549 |
> |
*/ |
| 550 |
|
void ForceMatrixDecomposition::distributeIntermediateData() { |
| 551 |
|
snap_ = sman_->getCurrentSnapshot(); |
| 552 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 588 |
|
|
| 589 |
|
if (storageLayout_ & DataStorage::dslTorque) { |
| 590 |
|
|
| 591 |
< |
int nt = snap_->atomData.force.size(); |
| 591 |
> |
int nt = snap_->atomData.torque.size(); |
| 592 |
|
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 593 |
|
|
| 594 |
|
AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 595 |
< |
for (int i = 0; i < n; i++) { |
| 595 |
> |
for (int i = 0; i < nt; i++) { |
| 596 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 597 |
|
trq_tmp[i] = 0.0; |
| 598 |
|
} |
| 599 |
|
|
| 600 |
|
AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 601 |
< |
for (int i = 0; i < n; i++) |
| 601 |
> |
for (int i = 0; i < nt; i++) |
| 602 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 603 |
|
} |
| 231 |
– |
|
| 232 |
– |
int nLocal = snap_->getNumberOfAtoms(); |
| 604 |
|
|
| 605 |
< |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 606 |
< |
vector<RealType> (nLocal, 0.0)); |
| 607 |
< |
|
| 608 |
< |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 609 |
< |
AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
| 610 |
< |
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 611 |
< |
pot_local[i] += pot_temp[i][ii]; |
| 605 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 606 |
> |
|
| 607 |
> |
int ns = snap_->atomData.skippedCharge.size(); |
| 608 |
> |
vector<RealType> skch_tmp(ns, 0.0); |
| 609 |
> |
|
| 610 |
> |
AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
| 611 |
> |
for (int i = 0; i < ns; i++) { |
| 612 |
> |
snap_->atomData.skippedCharge[i] = skch_tmp[i]; |
| 613 |
> |
skch_tmp[i] = 0.0; |
| 614 |
|
} |
| 615 |
+ |
|
| 616 |
+ |
AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
| 617 |
+ |
for (int i = 0; i < ns; i++) |
| 618 |
+ |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 619 |
|
} |
| 620 |
+ |
|
| 621 |
+ |
nLocal_ = snap_->getNumberOfAtoms(); |
| 622 |
+ |
|
| 623 |
+ |
vector<potVec> pot_temp(nLocal_, |
| 624 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 625 |
+ |
|
| 626 |
+ |
// scatter/gather pot_row into the members of my column |
| 627 |
+ |
|
| 628 |
+ |
AtomCommPotRow->scatter(pot_row, pot_temp); |
| 629 |
+ |
|
| 630 |
+ |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 631 |
+ |
pairwisePot += pot_temp[ii]; |
| 632 |
+ |
|
| 633 |
+ |
fill(pot_temp.begin(), pot_temp.end(), |
| 634 |
+ |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 635 |
+ |
|
| 636 |
+ |
AtomCommPotColumn->scatter(pot_col, pot_temp); |
| 637 |
+ |
|
| 638 |
+ |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 639 |
+ |
pairwisePot += pot_temp[ii]; |
| 640 |
|
#endif |
| 641 |
+ |
|
| 642 |
|
} |
| 643 |
|
|
| 644 |
+ |
int ForceMatrixDecomposition::getNAtomsInRow() { |
| 645 |
+ |
#ifdef IS_MPI |
| 646 |
+ |
return nAtomsInRow_; |
| 647 |
+ |
#else |
| 648 |
+ |
return nLocal_; |
| 649 |
+ |
#endif |
| 650 |
+ |
} |
| 651 |
+ |
|
| 652 |
+ |
/** |
| 653 |
+ |
* returns the list of atoms belonging to this group. |
| 654 |
+ |
*/ |
| 655 |
+ |
vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){ |
| 656 |
+ |
#ifdef IS_MPI |
| 657 |
+ |
return groupListRow_[cg1]; |
| 658 |
+ |
#else |
| 659 |
+ |
return groupList_[cg1]; |
| 660 |
+ |
#endif |
| 661 |
+ |
} |
| 662 |
+ |
|
| 663 |
+ |
vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){ |
| 664 |
+ |
#ifdef IS_MPI |
| 665 |
+ |
return groupListCol_[cg2]; |
| 666 |
+ |
#else |
| 667 |
+ |
return groupList_[cg2]; |
| 668 |
+ |
#endif |
| 669 |
+ |
} |
| 670 |
|
|
| 671 |
|
Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ |
| 672 |
|
Vector3d d; |
| 708 |
|
snap_->wrapVector(d); |
| 709 |
|
return d; |
| 710 |
|
} |
| 711 |
+ |
|
| 712 |
+ |
RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) { |
| 713 |
+ |
#ifdef IS_MPI |
| 714 |
+ |
return massFactorsRow[atom1]; |
| 715 |
+ |
#else |
| 716 |
+ |
return massFactors[atom1]; |
| 717 |
+ |
#endif |
| 718 |
+ |
} |
| 719 |
+ |
|
| 720 |
+ |
RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) { |
| 721 |
+ |
#ifdef IS_MPI |
| 722 |
+ |
return massFactorsCol[atom2]; |
| 723 |
+ |
#else |
| 724 |
+ |
return massFactors[atom2]; |
| 725 |
+ |
#endif |
| 726 |
+ |
|
| 727 |
+ |
} |
| 728 |
|
|
| 729 |
|
Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ |
| 730 |
|
Vector3d d; |
| 739 |
|
return d; |
| 740 |
|
} |
| 741 |
|
|
| 742 |
+ |
vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) { |
| 743 |
+ |
return excludesForAtom[atom1]; |
| 744 |
+ |
} |
| 745 |
+ |
|
| 746 |
+ |
/** |
| 747 |
+ |
* We need to exclude some overcounted interactions that result from |
| 748 |
+ |
* the parallel decomposition. |
| 749 |
+ |
*/ |
| 750 |
+ |
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 751 |
+ |
int unique_id_1, unique_id_2; |
| 752 |
+ |
|
| 753 |
+ |
#ifdef IS_MPI |
| 754 |
+ |
// in MPI, we have to look up the unique IDs for each atom |
| 755 |
+ |
unique_id_1 = AtomRowToGlobal[atom1]; |
| 756 |
+ |
unique_id_2 = AtomColToGlobal[atom2]; |
| 757 |
+ |
|
| 758 |
+ |
// this situation should only arise in MPI simulations |
| 759 |
+ |
if (unique_id_1 == unique_id_2) return true; |
| 760 |
+ |
|
| 761 |
+ |
// this prevents us from doing the pair on multiple processors |
| 762 |
+ |
if (unique_id_1 < unique_id_2) { |
| 763 |
+ |
if ((unique_id_1 + unique_id_2) % 2 == 0) return true; |
| 764 |
+ |
} else { |
| 765 |
+ |
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 766 |
+ |
} |
| 767 |
+ |
#endif |
| 768 |
+ |
return false; |
| 769 |
+ |
} |
| 770 |
+ |
|
| 771 |
+ |
/** |
| 772 |
+ |
* We need to handle the interactions for atoms who are involved in |
| 773 |
+ |
* the same rigid body as well as some short range interactions |
| 774 |
+ |
* (bonds, bends, torsions) differently from other interactions. |
| 775 |
+ |
* We'll still visit the pairwise routines, but with a flag that |
| 776 |
+ |
* tells those routines to exclude the pair from direct long range |
| 777 |
+ |
* interactions. Some indirect interactions (notably reaction |
| 778 |
+ |
* field) must still be handled for these pairs. |
| 779 |
+ |
*/ |
| 780 |
+ |
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
| 781 |
+ |
int unique_id_2; |
| 782 |
+ |
|
| 783 |
+ |
#ifdef IS_MPI |
| 784 |
+ |
// in MPI, we have to look up the unique IDs for the row atom. |
| 785 |
+ |
unique_id_2 = AtomColToGlobal[atom2]; |
| 786 |
+ |
#else |
| 787 |
+ |
// in the normal loop, the atom numbers are unique |
| 788 |
+ |
unique_id_2 = atom2; |
| 789 |
+ |
#endif |
| 790 |
+ |
|
| 791 |
+ |
for (vector<int>::iterator i = excludesForAtom[atom1].begin(); |
| 792 |
+ |
i != excludesForAtom[atom1].end(); ++i) { |
| 793 |
+ |
if ( (*i) == unique_id_2 ) return true; |
| 794 |
+ |
} |
| 795 |
+ |
|
| 796 |
+ |
return false; |
| 797 |
+ |
} |
| 798 |
+ |
|
| 799 |
+ |
|
| 800 |
|
void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ |
| 801 |
|
#ifdef IS_MPI |
| 802 |
|
atomRowData.force[atom1] += fg; |
| 811 |
|
#else |
| 812 |
|
snap_->atomData.force[atom2] += fg; |
| 813 |
|
#endif |
| 315 |
– |
|
| 814 |
|
} |
| 815 |
|
|
| 816 |
|
// filling interaction blocks with pointers |
| 817 |
< |
InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
| 817 |
> |
void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, |
| 818 |
> |
int atom1, int atom2) { |
| 819 |
|
|
| 820 |
< |
InteractionData idat; |
| 820 |
> |
idat.excluded = excludeAtomPair(atom1, atom2); |
| 821 |
> |
|
| 822 |
|
#ifdef IS_MPI |
| 823 |
+ |
|
| 824 |
+ |
idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 825 |
+ |
ff_->getAtomType(identsCol[atom2]) ); |
| 826 |
+ |
|
| 827 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 828 |
|
idat.A1 = &(atomRowData.aMat[atom1]); |
| 829 |
|
idat.A2 = &(atomColData.aMat[atom2]); |
| 830 |
|
} |
| 831 |
< |
|
| 831 |
> |
|
| 832 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 833 |
|
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 834 |
|
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 844 |
|
idat.rho2 = &(atomColData.density[atom2]); |
| 845 |
|
} |
| 846 |
|
|
| 847 |
+ |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 848 |
+ |
idat.frho1 = &(atomRowData.functional[atom1]); |
| 849 |
+ |
idat.frho2 = &(atomColData.functional[atom2]); |
| 850 |
+ |
} |
| 851 |
+ |
|
| 852 |
|
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 853 |
|
idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 854 |
|
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 855 |
|
} |
| 856 |
+ |
|
| 857 |
+ |
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 858 |
+ |
idat.particlePot1 = &(atomRowData.particlePot[atom1]); |
| 859 |
+ |
idat.particlePot2 = &(atomColData.particlePot[atom2]); |
| 860 |
+ |
} |
| 861 |
+ |
|
| 862 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 863 |
+ |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 864 |
+ |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 865 |
+ |
} |
| 866 |
+ |
|
| 867 |
|
#else |
| 868 |
+ |
|
| 869 |
+ |
idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 870 |
+ |
ff_->getAtomType(idents[atom2]) ); |
| 871 |
+ |
|
| 872 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 873 |
|
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 874 |
|
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 884 |
|
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 885 |
|
} |
| 886 |
|
|
| 887 |
< |
if (storageLayout_ & DataStorage::dslDensity) { |
| 887 |
> |
if (storageLayout_ & DataStorage::dslDensity) { |
| 888 |
|
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 889 |
|
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 890 |
|
} |
| 891 |
|
|
| 892 |
+ |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 893 |
+ |
idat.frho1 = &(snap_->atomData.functional[atom1]); |
| 894 |
+ |
idat.frho2 = &(snap_->atomData.functional[atom2]); |
| 895 |
+ |
} |
| 896 |
+ |
|
| 897 |
|
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 898 |
|
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 899 |
|
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 900 |
|
} |
| 901 |
+ |
|
| 902 |
+ |
if (storageLayout_ & DataStorage::dslParticlePot) { |
| 903 |
+ |
idat.particlePot1 = &(snap_->atomData.particlePot[atom1]); |
| 904 |
+ |
idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
| 905 |
+ |
} |
| 906 |
+ |
|
| 907 |
+ |
if (storageLayout_ & DataStorage::dslSkippedCharge) { |
| 908 |
+ |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 909 |
+ |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 910 |
+ |
} |
| 911 |
|
#endif |
| 373 |
– |
|
| 912 |
|
} |
| 913 |
< |
InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
| 914 |
< |
InteractionData idat; |
| 915 |
< |
skippedCharge1 |
| 378 |
< |
skippedCharge2 |
| 379 |
< |
rij |
| 380 |
< |
d |
| 381 |
< |
electroMult |
| 382 |
< |
sw |
| 383 |
< |
f |
| 913 |
> |
|
| 914 |
> |
|
| 915 |
> |
void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
| 916 |
|
#ifdef IS_MPI |
| 917 |
+ |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 918 |
+ |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 919 |
|
|
| 920 |
< |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 921 |
< |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 922 |
< |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 923 |
< |
} |
| 390 |
< |
if (storageLayout_ & DataStorage::dslTorque) { |
| 391 |
< |
idat.t1 = &(atomRowData.torque[atom1]); |
| 392 |
< |
idat.t2 = &(atomColData.torque[atom2]); |
| 393 |
< |
} |
| 920 |
> |
atomRowData.force[atom1] += *(idat.f1); |
| 921 |
> |
atomColData.force[atom2] -= *(idat.f1); |
| 922 |
> |
#else |
| 923 |
> |
pairwisePot += *(idat.pot); |
| 924 |
|
|
| 925 |
+ |
snap_->atomData.force[atom1] += *(idat.f1); |
| 926 |
+ |
snap_->atomData.force[atom2] -= *(idat.f1); |
| 927 |
+ |
#endif |
| 928 |
|
|
| 929 |
|
} |
| 397 |
– |
SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
| 398 |
– |
} |
| 930 |
|
|
| 400 |
– |
|
| 931 |
|
/* |
| 932 |
|
* buildNeighborList |
| 933 |
|
* |
| 934 |
|
* first element of pair is row-indexed CutoffGroup |
| 935 |
|
* second element of pair is column-indexed CutoffGroup |
| 936 |
|
*/ |
| 937 |
< |
vector<pair<int, int> > buildNeighborList() { |
| 938 |
< |
Vector3d dr, invWid, rs, shift; |
| 939 |
< |
Vector3i cc, m1v, m2s; |
| 940 |
< |
RealType rrNebr; |
| 941 |
< |
int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset; |
| 937 |
> |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 938 |
> |
|
| 939 |
> |
vector<pair<int, int> > neighborList; |
| 940 |
> |
groupCutoffs cuts; |
| 941 |
> |
bool doAllPairs = false; |
| 942 |
|
|
| 943 |
+ |
#ifdef IS_MPI |
| 944 |
+ |
cellListRow_.clear(); |
| 945 |
+ |
cellListCol_.clear(); |
| 946 |
+ |
#else |
| 947 |
+ |
cellList_.clear(); |
| 948 |
+ |
#endif |
| 949 |
|
|
| 950 |
< |
vector<pair<int, int> > neighborList; |
| 951 |
< |
Vector3i nCells; |
| 952 |
< |
Vector3d invWid, r; |
| 417 |
< |
|
| 418 |
< |
rList_ = (rCut_ + skinThickness_); |
| 419 |
< |
rl2 = rList_ * rList_; |
| 420 |
< |
|
| 421 |
< |
snap_ = sman_->getCurrentSnapshot(); |
| 950 |
> |
RealType rList_ = (largestRcut_ + skinThickness_); |
| 951 |
> |
RealType rl2 = rList_ * rList_; |
| 952 |
> |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 953 |
|
Mat3x3d Hmat = snap_->getHmat(); |
| 954 |
|
Vector3d Hx = Hmat.getColumn(0); |
| 955 |
|
Vector3d Hy = Hmat.getColumn(1); |
| 956 |
|
Vector3d Hz = Hmat.getColumn(2); |
| 957 |
|
|
| 958 |
< |
nCells.x() = (int) ( Hx.length() )/ rList_; |
| 959 |
< |
nCells.y() = (int) ( Hy.length() )/ rList_; |
| 960 |
< |
nCells.z() = (int) ( Hz.length() )/ rList_; |
| 958 |
> |
nCells_.x() = (int) ( Hx.length() )/ rList_; |
| 959 |
> |
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 960 |
> |
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 961 |
|
|
| 962 |
< |
for (i = 0; i < nGroupsInRow; i++) { |
| 432 |
< |
rs = cgRowData.position[i]; |
| 433 |
< |
snap_->scaleVector(rs); |
| 434 |
< |
} |
| 962 |
> |
// handle small boxes where the cell offsets can end up repeating cells |
| 963 |
|
|
| 964 |
+ |
if (nCells_.x() < 3) doAllPairs = true; |
| 965 |
+ |
if (nCells_.y() < 3) doAllPairs = true; |
| 966 |
+ |
if (nCells_.z() < 3) doAllPairs = true; |
| 967 |
|
|
| 968 |
< |
VDiv (invWid, cells, region); |
| 969 |
< |
for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1; |
| 970 |
< |
for (n = 0; n < nMol; n ++) { |
| 971 |
< |
VSAdd (rs, mol[n].r, 0.5, region); |
| 972 |
< |
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(); |
| 968 |
> |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 969 |
> |
Vector3d rs, scaled, dr; |
| 970 |
> |
Vector3i whichCell; |
| 971 |
> |
int cellIndex; |
| 972 |
> |
int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
| 973 |
|
|
| 974 |
< |
if (m2v.x() >= cells.x) { |
| 975 |
< |
m2v.x() = 0; |
| 976 |
< |
shift.x() = region.x(); |
| 977 |
< |
} else if (m2v.x() < 0) { |
| 978 |
< |
m2v.x() = cells.x() - 1; |
| 979 |
< |
shift.x() = - region.x(); |
| 462 |
< |
} |
| 974 |
> |
#ifdef IS_MPI |
| 975 |
> |
cellListRow_.resize(nCtot); |
| 976 |
> |
cellListCol_.resize(nCtot); |
| 977 |
> |
#else |
| 978 |
> |
cellList_.resize(nCtot); |
| 979 |
> |
#endif |
| 980 |
|
|
| 981 |
< |
if (m2v.y() >= cells.y()) { |
| 982 |
< |
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 |
< |
} |
| 981 |
> |
if (!doAllPairs) { |
| 982 |
> |
#ifdef IS_MPI |
| 983 |
|
|
| 984 |
< |
m2 = VLinear (m2v, cells) + nMol; |
| 985 |
< |
for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) { |
| 986 |
< |
for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) { |
| 987 |
< |
if (m1 != m2 || j2 < j1) { |
| 988 |
< |
dr = mol[j1].r - mol[j2].r; |
| 989 |
< |
VSub (dr, mol[j1].r, mol[j2].r); |
| 990 |
< |
VVSub (dr, shift); |
| 991 |
< |
if (VLenSq (dr) < rrNebr) { |
| 992 |
< |
neighborList.push_back(make_pair(j1, j2)); |
| 984 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 985 |
> |
rs = cgRowData.position[i]; |
| 986 |
> |
|
| 987 |
> |
// scaled positions relative to the box vectors |
| 988 |
> |
scaled = invHmat * rs; |
| 989 |
> |
|
| 990 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 991 |
> |
// numbers |
| 992 |
> |
for (int j = 0; j < 3; j++) { |
| 993 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 994 |
> |
scaled[j] += 0.5; |
| 995 |
> |
} |
| 996 |
> |
|
| 997 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 998 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 999 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1000 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1001 |
> |
|
| 1002 |
> |
// find single index of this cell: |
| 1003 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1004 |
> |
|
| 1005 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1006 |
> |
cellListRow_[cellIndex].push_back(i); |
| 1007 |
> |
} |
| 1008 |
> |
|
| 1009 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 1010 |
> |
rs = cgColData.position[i]; |
| 1011 |
> |
|
| 1012 |
> |
// scaled positions relative to the box vectors |
| 1013 |
> |
scaled = invHmat * rs; |
| 1014 |
> |
|
| 1015 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1016 |
> |
// numbers |
| 1017 |
> |
for (int j = 0; j < 3; j++) { |
| 1018 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1019 |
> |
scaled[j] += 0.5; |
| 1020 |
> |
} |
| 1021 |
> |
|
| 1022 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1023 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1024 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1025 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1026 |
> |
|
| 1027 |
> |
// find single index of this cell: |
| 1028 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1029 |
> |
|
| 1030 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1031 |
> |
cellListCol_[cellIndex].push_back(i); |
| 1032 |
> |
} |
| 1033 |
> |
#else |
| 1034 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 1035 |
> |
rs = snap_->cgData.position[i]; |
| 1036 |
> |
|
| 1037 |
> |
// scaled positions relative to the box vectors |
| 1038 |
> |
scaled = invHmat * rs; |
| 1039 |
> |
|
| 1040 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1041 |
> |
// numbers |
| 1042 |
> |
for (int j = 0; j < 3; j++) { |
| 1043 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1044 |
> |
scaled[j] += 0.5; |
| 1045 |
> |
} |
| 1046 |
> |
|
| 1047 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1048 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1049 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1050 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1051 |
> |
|
| 1052 |
> |
// find single index of this cell: |
| 1053 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1054 |
> |
|
| 1055 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1056 |
> |
cellList_[cellIndex].push_back(i); |
| 1057 |
> |
} |
| 1058 |
> |
#endif |
| 1059 |
> |
|
| 1060 |
> |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 1061 |
> |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 1062 |
> |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 1063 |
> |
Vector3i m1v(m1x, m1y, m1z); |
| 1064 |
> |
int m1 = Vlinear(m1v, nCells_); |
| 1065 |
> |
|
| 1066 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 1067 |
> |
os != cellOffsets_.end(); ++os) { |
| 1068 |
> |
|
| 1069 |
> |
Vector3i m2v = m1v + (*os); |
| 1070 |
> |
|
| 1071 |
> |
if (m2v.x() >= nCells_.x()) { |
| 1072 |
> |
m2v.x() = 0; |
| 1073 |
> |
} else if (m2v.x() < 0) { |
| 1074 |
> |
m2v.x() = nCells_.x() - 1; |
| 1075 |
> |
} |
| 1076 |
> |
|
| 1077 |
> |
if (m2v.y() >= nCells_.y()) { |
| 1078 |
> |
m2v.y() = 0; |
| 1079 |
> |
} else if (m2v.y() < 0) { |
| 1080 |
> |
m2v.y() = nCells_.y() - 1; |
| 1081 |
> |
} |
| 1082 |
> |
|
| 1083 |
> |
if (m2v.z() >= nCells_.z()) { |
| 1084 |
> |
m2v.z() = 0; |
| 1085 |
> |
} else if (m2v.z() < 0) { |
| 1086 |
> |
m2v.z() = nCells_.z() - 1; |
| 1087 |
> |
} |
| 1088 |
> |
|
| 1089 |
> |
int m2 = Vlinear (m2v, nCells_); |
| 1090 |
> |
|
| 1091 |
> |
#ifdef IS_MPI |
| 1092 |
> |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1093 |
> |
j1 != cellListRow_[m1].end(); ++j1) { |
| 1094 |
> |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1095 |
> |
j2 != cellListCol_[m2].end(); ++j2) { |
| 1096 |
> |
|
| 1097 |
> |
// Always do this if we're in different cells or if |
| 1098 |
> |
// we're in the same cell and the global index of the |
| 1099 |
> |
// j2 cutoff group is less than the j1 cutoff group |
| 1100 |
> |
|
| 1101 |
> |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 1102 |
> |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 1103 |
> |
snap_->wrapVector(dr); |
| 1104 |
> |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1105 |
> |
if (dr.lengthSquare() < cuts.third) { |
| 1106 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1107 |
> |
} |
| 1108 |
|
} |
| 1109 |
|
} |
| 1110 |
|
} |
| 1111 |
+ |
#else |
| 1112 |
+ |
|
| 1113 |
+ |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 1114 |
+ |
j1 != cellList_[m1].end(); ++j1) { |
| 1115 |
+ |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 1116 |
+ |
j2 != cellList_[m2].end(); ++j2) { |
| 1117 |
+ |
|
| 1118 |
+ |
// Always do this if we're in different cells or if |
| 1119 |
+ |
// we're in the same cell and the global index of the |
| 1120 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 1121 |
+ |
|
| 1122 |
+ |
if (m2 != m1 || (*j2) < (*j1)) { |
| 1123 |
+ |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1124 |
+ |
snap_->wrapVector(dr); |
| 1125 |
+ |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1126 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1127 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1128 |
+ |
} |
| 1129 |
+ |
} |
| 1130 |
+ |
} |
| 1131 |
+ |
} |
| 1132 |
+ |
#endif |
| 1133 |
|
} |
| 1134 |
|
} |
| 1135 |
|
} |
| 1136 |
|
} |
| 1137 |
+ |
} else { |
| 1138 |
+ |
// branch to do all cutoff group pairs |
| 1139 |
+ |
#ifdef IS_MPI |
| 1140 |
+ |
for (int j1 = 0; j1 < nGroupsInRow_; j1++) { |
| 1141 |
+ |
for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
| 1142 |
+ |
dr = cgColData.position[j2] - cgRowData.position[j1]; |
| 1143 |
+ |
snap_->wrapVector(dr); |
| 1144 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1145 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1146 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1147 |
+ |
} |
| 1148 |
+ |
} |
| 1149 |
+ |
} |
| 1150 |
+ |
#else |
| 1151 |
+ |
for (int j1 = 0; j1 < nGroups_ - 1; j1++) { |
| 1152 |
+ |
for (int j2 = j1 + 1; j2 < nGroups_; j2++) { |
| 1153 |
+ |
dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; |
| 1154 |
+ |
snap_->wrapVector(dr); |
| 1155 |
+ |
cuts = getGroupCutoffs( j1, j2 ); |
| 1156 |
+ |
if (dr.lengthSquare() < cuts.third) { |
| 1157 |
+ |
neighborList.push_back(make_pair(j1, j2)); |
| 1158 |
+ |
} |
| 1159 |
+ |
} |
| 1160 |
+ |
} |
| 1161 |
+ |
#endif |
| 1162 |
|
} |
| 1163 |
+ |
|
| 1164 |
+ |
// save the local cutoff group positions for the check that is |
| 1165 |
+ |
// done on each loop: |
| 1166 |
+ |
saved_CG_positions_.clear(); |
| 1167 |
+ |
for (int i = 0; i < nGroups_; i++) |
| 1168 |
+ |
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 1169 |
+ |
|
| 1170 |
+ |
return neighborList; |
| 1171 |
|
} |
| 490 |
– |
|
| 491 |
– |
|
| 1172 |
|
} //end namespace OpenMD |
