# | Line 759 | Line 759 | namespace OpenMD { | |
---|---|---|
759 | if ( simParams_->getAccumulateBoxDipole() ) { | |
760 | calcBoxDipole_ = true; | |
761 | } | |
762 | < | |
762 | > | |
763 | set<AtomType*>::iterator i; | |
764 | set<AtomType*> atomTypes; | |
765 | atomTypes = getSimulatedAtomTypes(); | |
# | Line 772 | Line 772 | namespace OpenMD { | |
772 | usesMetallic |= (*i)->isMetal(); | |
773 | usesDirectional |= (*i)->isDirectional(); | |
774 | } | |
775 | < | |
775 | > | |
776 | #ifdef IS_MPI | |
777 | int temp; | |
778 | temp = usesDirectional; | |
779 | MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
780 | < | |
780 | > | |
781 | temp = usesMetallic; | |
782 | MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
783 | < | |
783 | > | |
784 | temp = usesElectrostatic; | |
785 | MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
786 | + | #else |
787 | + | |
788 | + | usesDirectionalAtoms_ = usesDirectional; |
789 | + | usesMetallicAtoms_ = usesMetallic; |
790 | + | usesElectrostaticAtoms_ = usesElectrostatic; |
791 | + | |
792 | #endif | |
793 | + | |
794 | + | requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
795 | + | requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
796 | + | requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
797 | } | |
798 | ||
799 | ||
# | Line 838 | Line 848 | namespace OpenMD { | |
848 | Atom* atom; | |
849 | RealType totalMass; | |
850 | ||
851 | < | //to avoid memory reallocation, reserve enough space for massFactors_ |
852 | < | massFactors_.clear(); |
853 | < | massFactors_.reserve(getNCutoffGroups()); |
851 | > | /** |
852 | > | * The mass factor is the relative mass of an atom to the total |
853 | > | * mass of the cutoff group it belongs to. By default, all atoms |
854 | > | * are their own cutoff groups, and therefore have mass factors of |
855 | > | * 1. We need some special handling for massless atoms, which |
856 | > | * will be treated as carrying the entire mass of the cutoff |
857 | > | * group. |
858 | > | */ |
859 | > | massFactors_.clear(); |
860 | > | massFactors_.resize(getNAtoms(), 1.0); |
861 | ||
862 | + | cerr << "mfs in si = " << massFactors_.size() << "\n"; |
863 | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { | |
864 | for (cg = mol->beginCutoffGroup(ci); cg != NULL; | |
865 | cg = mol->nextCutoffGroup(ci)) { | |
# | Line 849 | Line 867 | namespace OpenMD { | |
867 | totalMass = cg->getMass(); | |
868 | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { | |
869 | // Check for massless groups - set mfact to 1 if true | |
870 | < | if (totalMass != 0) |
871 | < | massFactors_.push_back(atom->getMass()/totalMass); |
870 | > | if (totalMass != 0) |
871 | > | massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
872 | else | |
873 | < | massFactors_.push_back( 1.0 ); |
873 | > | massFactors_[atom->getLocalIndex()] = 1.0; |
874 | } | |
875 | } | |
876 | } | |
# | Line 879 | Line 897 | namespace OpenMD { | |
897 | int* oneThreeList = oneThreeInteractions_.getPairList(); | |
898 | int* oneFourList = oneFourInteractions_.getPairList(); | |
899 | ||
882 | – | //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
883 | – | // &nExclude, excludeList, |
884 | – | // &nOneTwo, oneTwoList, |
885 | – | // &nOneThree, oneThreeList, |
886 | – | // &nOneFour, oneFourList, |
887 | – | // &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
888 | – | // &fortranGlobalGroupMembership[0], &isError); |
889 | – | |
900 | topologyDone_ = true; | |
901 | } | |
902 |
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