| 73 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 74 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
| 75 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
| 76 |
< |
sman_(NULL), fortranInitialized_(false), selectMan_(NULL) { |
| 76 |
> |
sman_(NULL), fortranInitialized_(false) { |
| 77 |
|
|
| 78 |
|
|
| 79 |
|
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
| 139 |
|
molToProcMap_.resize(nGlobalMols_); |
| 140 |
|
#endif |
| 141 |
|
|
| 142 |
– |
selectMan_ = new SelectionManager(this); |
| 143 |
– |
selectMan_->selectAll(); |
| 142 |
|
} |
| 143 |
|
|
| 144 |
|
SimInfo::~SimInfo() { |
| 145 |
< |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
| 146 |
< |
|
| 147 |
< |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
| 145 |
> |
std::map<int, Molecule*>::iterator i; |
| 146 |
> |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
| 147 |
> |
delete i->second; |
| 148 |
> |
} |
| 149 |
> |
molecules_.clear(); |
| 150 |
> |
|
| 151 |
> |
MemoryUtils::deletePointers(moleculeStamps_); |
| 152 |
|
|
| 153 |
|
delete sman_; |
| 154 |
|
delete simParams_; |
| 155 |
|
delete forceField_; |
| 154 |
– |
delete selectMan_; |
| 156 |
|
} |
| 157 |
|
|
| 158 |
|
int SimInfo::getNGlobalConstraints() { |
| 367 |
|
exclude_.addPair(c, d); |
| 368 |
|
} |
| 369 |
|
|
| 370 |
< |
|
| 370 |
> |
Molecule::RigidBodyIterator rbIter; |
| 371 |
> |
RigidBody* rb; |
| 372 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 373 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 374 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 375 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 376 |
> |
a = atoms[i]->getGlobalIndex(); |
| 377 |
> |
b = atoms[j]->getGlobalIndex(); |
| 378 |
> |
exclude_.addPair(a, b); |
| 379 |
> |
} |
| 380 |
> |
} |
| 381 |
> |
} |
| 382 |
> |
|
| 383 |
> |
Molecule::CutoffGroupIterator cgIter; |
| 384 |
> |
CutoffGroup* cg; |
| 385 |
> |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 386 |
> |
std::vector<Atom*> atoms = cg->getAtoms(); |
| 387 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 388 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 389 |
> |
a = atoms[i]->getGlobalIndex(); |
| 390 |
> |
b = atoms[j]->getGlobalIndex(); |
| 391 |
> |
exclude_.addPair(a, b); |
| 392 |
> |
} |
| 393 |
> |
} |
| 394 |
> |
} |
| 395 |
> |
|
| 396 |
|
} |
| 397 |
|
|
| 398 |
|
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 436 |
|
exclude_.removePair(b, d); |
| 437 |
|
exclude_.removePair(c, d); |
| 438 |
|
} |
| 439 |
+ |
|
| 440 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 441 |
+ |
RigidBody* rb; |
| 442 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 443 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 444 |
+ |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 445 |
+ |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 446 |
+ |
a = atoms[i]->getGlobalIndex(); |
| 447 |
+ |
b = atoms[j]->getGlobalIndex(); |
| 448 |
+ |
exclude_.removePair(a, b); |
| 449 |
+ |
} |
| 450 |
+ |
} |
| 451 |
+ |
} |
| 452 |
|
|
| 453 |
+ |
Molecule::CutoffGroupIterator cgIter; |
| 454 |
+ |
CutoffGroup* cg; |
| 455 |
+ |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 456 |
+ |
std::vector<Atom*> atoms = cg->getAtoms(); |
| 457 |
+ |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 458 |
+ |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 459 |
+ |
a = atoms[i]->getGlobalIndex(); |
| 460 |
+ |
b = atoms[j]->getGlobalIndex(); |
| 461 |
+ |
exclude_.removePair(a, b); |
| 462 |
+ |
} |
| 463 |
+ |
} |
| 464 |
+ |
} |
| 465 |
+ |
|
| 466 |
|
} |
| 467 |
|
|
| 468 |
|
|
| 806 |
|
return maxCutoffRadius; |
| 807 |
|
} |
| 808 |
|
|
| 809 |
< |
void SimInfo::setupCutoff() { |
| 758 |
< |
double rcut_; //cutoff radius |
| 759 |
< |
double rsw_; //switching radius |
| 809 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
| 810 |
|
|
| 811 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 812 |
|
|
| 817 |
|
"\tfor the cutoffRadius.\n"); |
| 818 |
|
painCave.isFatal = 0; |
| 819 |
|
simError(); |
| 820 |
< |
rcut_ = 15.0; |
| 820 |
> |
rcut = 15.0; |
| 821 |
|
} else{ |
| 822 |
< |
rcut_ = simParams_->getRcut(); |
| 822 |
> |
rcut = simParams_->getRcut(); |
| 823 |
|
} |
| 824 |
|
|
| 825 |
|
if (!simParams_->haveRsw()){ |
| 829 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
| 830 |
|
painCave.isFatal = 0; |
| 831 |
|
simError(); |
| 832 |
< |
rsw_ = 0.95 * rcut_; |
| 832 |
> |
rsw = 0.95 * rcut; |
| 833 |
|
} else{ |
| 834 |
< |
rsw_ = simParams_->getRsw(); |
| 834 |
> |
rsw = simParams_->getRsw(); |
| 835 |
|
} |
| 836 |
|
|
| 837 |
|
} else { |
| 839 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 840 |
|
|
| 841 |
|
if (simParams_->haveRcut()) { |
| 842 |
< |
rcut_ = simParams_->getRcut(); |
| 842 |
> |
rcut = simParams_->getRcut(); |
| 843 |
|
} else { |
| 844 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 845 |
< |
rcut_ = calcMaxCutoffRadius(); |
| 845 |
> |
rcut = calcMaxCutoffRadius(); |
| 846 |
|
} |
| 847 |
|
|
| 848 |
|
if (simParams_->haveRsw()) { |
| 849 |
< |
rsw_ = simParams_->getRsw(); |
| 849 |
> |
rsw = simParams_->getRsw(); |
| 850 |
|
} else { |
| 851 |
< |
rsw_ = rcut_; |
| 851 |
> |
rsw = rcut; |
| 852 |
|
} |
| 853 |
|
|
| 854 |
|
} |
| 855 |
< |
|
| 855 |
> |
} |
| 856 |
> |
|
| 857 |
> |
void SimInfo::setupCutoff() { |
| 858 |
> |
getCutoff(rcut_, rsw_); |
| 859 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
| 860 |
|
|
| 861 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 887 |
|
} |
| 888 |
|
|
| 889 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 890 |
+ |
//if (sman_ == sman_) { |
| 891 |
+ |
// return; |
| 892 |
+ |
//} |
| 893 |
+ |
|
| 894 |
+ |
//delete sman_; |
| 895 |
|
sman_ = sman; |
| 896 |
|
|
| 897 |
|
Molecule* mol; |
