| 125 |
|
//equal to the total number of atoms minus number of atoms belong to |
| 126 |
|
//cutoff group defined in meta-data file plus the number of cutoff |
| 127 |
|
//groups defined in meta-data file |
| 128 |
– |
std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
| 129 |
– |
std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
| 130 |
– |
std::cerr << "nG = " << nGroups << "\n"; |
| 128 |
|
|
| 129 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 133 |
– |
|
| 134 |
– |
std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
| 130 |
|
|
| 131 |
|
//every free atom (atom does not belong to rigid bodies) is an |
| 132 |
|
//integrable object therefore the total number of integrable objects |
| 269 |
|
#endif |
| 270 |
|
return fdf_; |
| 271 |
|
} |
| 272 |
+ |
|
| 273 |
+ |
unsigned int SimInfo::getNLocalCutoffGroups(){ |
| 274 |
+ |
int nLocalCutoffAtoms = 0; |
| 275 |
+ |
Molecule* mol; |
| 276 |
+ |
MoleculeIterator mi; |
| 277 |
+ |
CutoffGroup* cg; |
| 278 |
+ |
Molecule::CutoffGroupIterator ci; |
| 279 |
|
|
| 280 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 281 |
+ |
|
| 282 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 283 |
+ |
cg = mol->nextCutoffGroup(ci)) { |
| 284 |
+ |
nLocalCutoffAtoms += cg->getNumAtom(); |
| 285 |
+ |
|
| 286 |
+ |
} |
| 287 |
+ |
} |
| 288 |
+ |
|
| 289 |
+ |
return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_; |
| 290 |
+ |
} |
| 291 |
+ |
|
| 292 |
|
void SimInfo::calcNdfRaw() { |
| 293 |
|
int ndfRaw_local; |
| 294 |
|
|
| 838 |
|
Atom* atom; |
| 839 |
|
RealType totalMass; |
| 840 |
|
|
| 841 |
< |
//to avoid memory reallocation, reserve enough space for massFactors_ |
| 841 |
> |
/** |
| 842 |
> |
* The mass factor is the relative mass of an atom to the total |
| 843 |
> |
* mass of the cutoff group it belongs to. By default, all atoms |
| 844 |
> |
* are their own cutoff groups, and therefore have mass factors of |
| 845 |
> |
* 1. We need some special handling for massless atoms, which |
| 846 |
> |
* will be treated as carrying the entire mass of the cutoff |
| 847 |
> |
* group. |
| 848 |
> |
*/ |
| 849 |
|
massFactors_.clear(); |
| 850 |
< |
massFactors_.reserve(getNCutoffGroups()); |
| 850 |
> |
massFactors_.resize(getNAtoms(), 1.0); |
| 851 |
|
|
| 852 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 853 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 856 |
|
totalMass = cg->getMass(); |
| 857 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 858 |
|
// Check for massless groups - set mfact to 1 if true |
| 859 |
< |
if (totalMass != 0) |
| 860 |
< |
massFactors_.push_back(atom->getMass()/totalMass); |
| 859 |
> |
if (totalMass != 0) |
| 860 |
> |
massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
| 861 |
|
else |
| 862 |
< |
massFactors_.push_back( 1.0 ); |
| 862 |
> |
massFactors_[atom->getLocalIndex()] = 1.0; |
| 863 |
|
} |
| 864 |
|
} |
| 865 |
|
} |
| 886 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 887 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 888 |
|
|
| 868 |
– |
//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 869 |
– |
// &nExclude, excludeList, |
| 870 |
– |
// &nOneTwo, oneTwoList, |
| 871 |
– |
// &nOneThree, oneThreeList, |
| 872 |
– |
// &nOneFour, oneFourList, |
| 873 |
– |
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 874 |
– |
// &fortranGlobalGroupMembership[0], &isError); |
| 875 |
– |
|
| 889 |
|
topologyDone_ = true; |
| 890 |
|
} |
| 891 |
|
|
