# | Line 125 | Line 125 | namespace OpenMD { | |
---|---|---|
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 | |
# | Line 274 | Line 269 | namespace OpenMD { | |
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 | ||
# | Line 824 | Line 838 | namespace OpenMD { | |
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; | |
# | Line 835 | Line 856 | namespace OpenMD { | |
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 | } | |
# | Line 865 | Line 886 | namespace OpenMD { | |
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 |
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