# | Line 55 | Line 55 | |
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55 | #include "primitives/Molecule.hpp" | |
56 | #include "primitives/StuntDouble.hpp" | |
57 | #include "UseTheForce/DarkSide/neighborLists_interface.h" | |
58 | + | #include "UseTheForce/doForces_interface.h" |
59 | #include "utils/MemoryUtils.hpp" | |
60 | #include "utils/simError.h" | |
61 | #include "selection/SelectionManager.hpp" | |
# | Line 131 | Line 132 | namespace OpenMD { | |
132 | //equal to the total number of atoms minus number of atoms belong to | |
133 | //cutoff group defined in meta-data file plus the number of cutoff | |
134 | //groups defined in meta-data file | |
135 | + | std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
136 | + | std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
137 | + | std::cerr << "nG = " << nGroups << "\n"; |
138 | + | |
139 | nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; | |
140 | + | |
141 | + | std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
142 | ||
143 | //every free atom (atom does not belong to rigid bodies) is an | |
144 | //integrable object therefore the total number of integrable objects | |
# | Line 817 | Line 824 | namespace OpenMD { | |
824 | } | |
825 | } | |
826 | ||
827 | < | //fill ident array of local atoms (it is actually ident of |
821 | < | //AtomType, it is so confusing !!!) |
822 | < | vector<int> identArray; |
827 | > | // Build the identArray_ |
828 | ||
829 | < | //to avoid memory reallocation, reserve enough space identArray |
830 | < | identArray.reserve(getNAtoms()); |
826 | < | |
829 | > | identArray_.clear(); |
830 | > | identArray_.reserve(getNAtoms()); |
831 | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { | |
832 | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { | |
833 | < | identArray.push_back(atom->getIdent()); |
833 | > | identArray_.push_back(atom->getIdent()); |
834 | } | |
835 | } | |
836 | ||
# | Line 924 | Line 928 | namespace OpenMD { | |
928 | sprintf(checkPointMsg, " mpiRefresh successful.\n"); | |
929 | errorCheckPoint(); | |
930 | #endif | |
931 | + | |
932 | + | initFortranFF(&isError); |
933 | + | if (isError) { |
934 | + | sprintf(painCave.errMsg, |
935 | + | "initFortranFF errror: fortran didn't like something we gave it.\n"); |
936 | + | painCave.isFatal = 1; |
937 | + | simError(); |
938 | + | } |
939 | fortranInitialized_ = true; | |
940 | } | |
941 | ||
# | Line 961 | Line 973 | namespace OpenMD { | |
973 | Molecule* mol; | |
974 | RigidBody* rb; | |
975 | Atom* atom; | |
976 | + | CutoffGroup* cg; |
977 | SimInfo::MoleculeIterator mi; | |
978 | Molecule::RigidBodyIterator rbIter; | |
979 | < | Molecule::AtomIterator atomIter;; |
979 | > | Molecule::AtomIterator atomIter; |
980 | > | Molecule::CutoffGroupIterator cgIter; |
981 | ||
982 | for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { | |
983 | ||
# | Line 973 | Line 987 | namespace OpenMD { | |
987 | ||
988 | for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { | |
989 | rb->setSnapshotManager(sman_); | |
990 | + | } |
991 | + | |
992 | + | for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
993 | + | cg->setSnapshotManager(sman_); |
994 | } | |
995 | } | |
996 |
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