| 803 |
|
Molecule::AtomIterator ai; |
| 804 |
|
Molecule::RigidBodyIterator ri; |
| 805 |
|
Molecule::CutoffGroupIterator ci; |
| 806 |
+ |
Molecule::BondIterator boi; |
| 807 |
+ |
Molecule::BendIterator bei; |
| 808 |
+ |
Molecule::TorsionIterator ti; |
| 809 |
+ |
Molecule::InversionIterator ii; |
| 810 |
|
Molecule::IntegrableObjectIterator ioi; |
| 811 |
< |
Molecule * mol; |
| 812 |
< |
Atom * atom; |
| 813 |
< |
RigidBody * rb; |
| 814 |
< |
CutoffGroup * cg; |
| 811 |
> |
Molecule* mol; |
| 812 |
> |
Atom* atom; |
| 813 |
> |
RigidBody* rb; |
| 814 |
> |
CutoffGroup* cg; |
| 815 |
> |
Bond* bond; |
| 816 |
> |
Bend* bend; |
| 817 |
> |
Torsion* torsion; |
| 818 |
> |
Inversion* inversion; |
| 819 |
|
int beginAtomIndex; |
| 820 |
|
int beginRigidBodyIndex; |
| 821 |
|
int beginCutoffGroupIndex; |
| 822 |
+ |
int beginBondIndex; |
| 823 |
+ |
int beginBendIndex; |
| 824 |
+ |
int beginTorsionIndex; |
| 825 |
+ |
int beginInversionIndex; |
| 826 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 827 |
|
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 828 |
|
|
| 829 |
|
beginAtomIndex = 0; |
| 830 |
< |
//rigidbody's index begins right after atom's |
| 830 |
> |
// The rigid body indices begin immediately after the atom indices: |
| 831 |
|
beginRigidBodyIndex = info->getNGlobalAtoms(); |
| 832 |
|
beginCutoffGroupIndex = 0; |
| 833 |
< |
|
| 833 |
> |
beginBondIndex = 0; |
| 834 |
> |
beginBendIndex = 0; |
| 835 |
> |
beginTorsionIndex = 0; |
| 836 |
> |
beginInversionIndex = 0; |
| 837 |
> |
|
| 838 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 839 |
|
|
| 840 |
|
#ifdef IS_MPI |
| 843 |
|
// stuff to do if I own this molecule |
| 844 |
|
mol = info->getMoleculeByGlobalIndex(i); |
| 845 |
|
|
| 846 |
< |
//local index(index in DataStorge) of atom is important |
| 847 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 846 |
> |
// The local index(index in DataStorge) of the atom is important: |
| 847 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 848 |
> |
atom = mol->nextAtom(ai)) { |
| 849 |
|
atom->setGlobalIndex(beginAtomIndex++); |
| 850 |
|
} |
| 851 |
|
|
| 854 |
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 855 |
|
} |
| 856 |
|
|
| 857 |
< |
//local index of cutoff group is trivial, it only depends on |
| 858 |
< |
//the order of travesing |
| 857 |
> |
// The local index of other objects only depends on the order |
| 858 |
> |
// of traversal: |
| 859 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 860 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 861 |
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 862 |
|
} |
| 863 |
+ |
for(bond = mol->beginBond(boi); bond != NULL; |
| 864 |
+ |
bond = mol->nextBond(boi)) { |
| 865 |
+ |
bond->setGlobalIndex(beginBondIndex++); |
| 866 |
+ |
} |
| 867 |
+ |
for(bend = mol->beginBend(bei); bend != NULL; |
| 868 |
+ |
bend = mol->nextBend(bei)) { |
| 869 |
+ |
bend->setGlobalIndex(beginBendIndex++); |
| 870 |
+ |
} |
| 871 |
+ |
for(torsion = mol->beginTorsion(ti); torsion != NULL; |
| 872 |
+ |
torsion = mol->nextTorsion(ti)) { |
| 873 |
+ |
torsion->setGlobalIndex(beginTorsionIndex++); |
| 874 |
+ |
} |
| 875 |
+ |
for(inversion = mol->beginInversion(ii); inversion != NULL; |
| 876 |
+ |
inversion = mol->nextInversion(ii)) { |
| 877 |
+ |
inversion->setGlobalIndex(beginInversionIndex++); |
| 878 |
+ |
} |
| 879 |
|
|
| 880 |
|
#ifdef IS_MPI |
| 881 |
|
} else { |
| 888 |
|
beginAtomIndex += stamp->getNAtoms(); |
| 889 |
|
beginRigidBodyIndex += stamp->getNRigidBodies(); |
| 890 |
|
beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
| 891 |
+ |
beginBondIndex += stamp->getNBonds(); |
| 892 |
+ |
beginBendIndex += stamp->getNBends(); |
| 893 |
+ |
beginTorsionIndex += stamp->getNTorsions(); |
| 894 |
+ |
beginInversionIndex += stamp->getNInversions(); |
| 895 |
|
} |
| 896 |
|
#endif |
| 897 |
|
|
| 899 |
|
|
| 900 |
|
//fill globalGroupMembership |
| 901 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 902 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 903 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 904 |
< |
|
| 902 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 903 |
> |
mol = info->nextMolecule(mi)) { |
| 904 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 905 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 906 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 907 |
|
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 908 |
|
} |
