# | Line 54 | Line 54 | |
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54 | #include "math/Vector3.hpp" | |
55 | #include "primitives/Molecule.hpp" | |
56 | #include "primitives/StuntDouble.hpp" | |
57 | – | #include "UseTheForce/DarkSide/neighborLists_interface.h" |
58 | – | #include "UseTheForce/doForces_interface.h" |
57 | #include "utils/MemoryUtils.hpp" | |
58 | #include "utils/simError.h" | |
59 | #include "selection/SelectionManager.hpp" | |
# | Line 63 | Line 61 | |
61 | #include "UseTheForce/ForceField.hpp" | |
62 | #include "nonbonded/SwitchingFunction.hpp" | |
63 | ||
66 | – | #ifdef IS_MPI |
67 | – | #include "UseTheForce/mpiComponentPlan.h" |
68 | – | #include "UseTheForce/DarkSide/simParallel_interface.h" |
69 | – | #endif |
70 | – | |
64 | using namespace std; | |
65 | namespace OpenMD { | |
66 | ||
# | Line 78 | Line 71 | namespace OpenMD { | |
71 | nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), | |
72 | nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), | |
73 | nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), | |
74 | < | nConstraints_(0), sman_(NULL), fortranInitialized_(false), |
74 | > | nConstraints_(0), sman_(NULL), topologyDone_(false), |
75 | calcBoxDipole_(false), useAtomicVirial_(true) { | |
76 | ||
77 | MoleculeStamp* molStamp; | |
# | Line 132 | 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 | |
135 | – | std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
136 | – | std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
137 | – | std::cerr << "nG = " << nGroups << "\n"; |
128 | ||
129 | nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; | |
140 | – | |
141 | – | 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 280 | Line 268 | namespace OpenMD { | |
268 | fdf_ = fdf_local; | |
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() { | |
# | Line 687 | Line 694 | namespace OpenMD { | |
694 | Atom* atom; | |
695 | set<AtomType*> atomTypes; | |
696 | ||
697 | < | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
698 | < | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
697 | > | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
698 | > | for(atom = mol->beginAtom(ai); atom != NULL; |
699 | > | atom = mol->nextAtom(ai)) { |
700 | atomTypes.insert(atom->getAtomType()); | |
701 | } | |
702 | } | |
703 | < | |
703 | > | |
704 | #ifdef IS_MPI | |
705 | ||
706 | // loop over the found atom types on this processor, and add their | |
707 | // numerical idents to a vector: | |
708 | < | |
708 | > | |
709 | vector<int> foundTypes; | |
710 | set<AtomType*>::iterator i; | |
711 | for (i = atomTypes.begin(); i != atomTypes.end(); ++i) | |
# | Line 706 | Line 714 | namespace OpenMD { | |
714 | // count_local holds the number of found types on this processor | |
715 | int count_local = foundTypes.size(); | |
716 | ||
717 | < | // count holds the total number of found types on all processors |
710 | < | // (some will be redundant with the ones found locally): |
711 | < | int count; |
712 | < | MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
717 | > | int nproc = MPI::COMM_WORLD.Get_size(); |
718 | ||
719 | < | // create a vector to hold the globally found types, and resize it: |
720 | < | vector<int> ftGlobal; |
721 | < | ftGlobal.resize(count); |
722 | < | vector<int> counts; |
719 | > | // we need arrays to hold the counts and displacement vectors for |
720 | > | // all processors |
721 | > | vector<int> counts(nproc, 0); |
722 | > | vector<int> disps(nproc, 0); |
723 | ||
724 | < | int nproc = MPI::COMM_WORLD.Get_size(); |
725 | < | counts.resize(nproc); |
726 | < | vector<int> disps; |
727 | < | disps.resize(nproc); |
724 | > | // fill the counts array |
725 | > | MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], |
726 | > | 1, MPI::INT); |
727 | > | |
728 | > | // use the processor counts to compute the displacement array |
729 | > | disps[0] = 0; |
730 | > | int totalCount = counts[0]; |
731 | > | for (int iproc = 1; iproc < nproc; iproc++) { |
732 | > | disps[iproc] = disps[iproc-1] + counts[iproc-1]; |
733 | > | totalCount += counts[iproc]; |
734 | > | } |
735 | ||
736 | < | // now spray out the foundTypes to all the other processors: |
736 | > | // we need a (possibly redundant) set of all found types: |
737 | > | vector<int> ftGlobal(totalCount); |
738 | ||
739 | + | // now spray out the foundTypes to all the other processors: |
740 | MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, | |
741 | < | &ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
741 | > | &ftGlobal[0], &counts[0], &disps[0], |
742 | > | MPI::INT); |
743 | ||
744 | + | vector<int>::iterator j; |
745 | + | |
746 | // foundIdents is a stl set, so inserting an already found ident | |
747 | // will have no effect. | |
748 | set<int> foundIdents; | |
749 | < | vector<int>::iterator j; |
749 | > | |
750 | for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) | |
751 | foundIdents.insert((*j)); | |
752 | ||
753 | // now iterate over the foundIdents and get the actual atom types | |
754 | // that correspond to these: | |
755 | set<int>::iterator it; | |
756 | < | for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
756 | > | for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
757 | atomTypes.insert( forceField_->getAtomType((*it)) ); | |
758 | ||
759 | #endif | |
760 | < | |
760 | > | |
761 | return atomTypes; | |
762 | } | |
763 | ||
# | Line 752 | Line 769 | namespace OpenMD { | |
769 | if ( simParams_->getAccumulateBoxDipole() ) { | |
770 | calcBoxDipole_ = true; | |
771 | } | |
772 | < | |
772 | > | |
773 | set<AtomType*>::iterator i; | |
774 | set<AtomType*> atomTypes; | |
775 | atomTypes = getSimulatedAtomTypes(); | |
# | Line 765 | Line 782 | namespace OpenMD { | |
782 | usesMetallic |= (*i)->isMetal(); | |
783 | usesDirectional |= (*i)->isDirectional(); | |
784 | } | |
785 | < | |
785 | > | |
786 | #ifdef IS_MPI | |
787 | int temp; | |
788 | temp = usesDirectional; | |
789 | MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
790 | < | |
790 | > | |
791 | temp = usesMetallic; | |
792 | MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
793 | < | |
793 | > | |
794 | temp = usesElectrostatic; | |
795 | MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
796 | + | #else |
797 | + | |
798 | + | usesDirectionalAtoms_ = usesDirectional; |
799 | + | usesMetallicAtoms_ = usesMetallic; |
800 | + | usesElectrostaticAtoms_ = usesElectrostatic; |
801 | + | |
802 | #endif | |
803 | < | fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; |
804 | < | fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; |
805 | < | fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; |
806 | < | fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; |
784 | < | fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
785 | < | fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
803 | > | |
804 | > | requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
805 | > | requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
806 | > | requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
807 | } | |
808 | ||
809 | < | void SimInfo::setupFortran() { |
810 | < | int isError; |
811 | < | int nExclude, nOneTwo, nOneThree, nOneFour; |
812 | < | vector<int> fortranGlobalGroupMembership; |
809 | > | |
810 | > | vector<int> SimInfo::getGlobalAtomIndices() { |
811 | > | SimInfo::MoleculeIterator mi; |
812 | > | Molecule* mol; |
813 | > | Molecule::AtomIterator ai; |
814 | > | Atom* atom; |
815 | > | |
816 | > | vector<int> GlobalAtomIndices(getNAtoms(), 0); |
817 | ||
818 | < | isError = 0; |
818 | > | for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
819 | > | |
820 | > | for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
821 | > | GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
822 | > | } |
823 | > | } |
824 | > | return GlobalAtomIndices; |
825 | > | } |
826 | ||
827 | < | //globalGroupMembership_ is filled by SimCreator |
828 | < | for (int i = 0; i < nGlobalAtoms_; i++) { |
829 | < | fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
827 | > | |
828 | > | vector<int> SimInfo::getGlobalGroupIndices() { |
829 | > | SimInfo::MoleculeIterator mi; |
830 | > | Molecule* mol; |
831 | > | Molecule::CutoffGroupIterator ci; |
832 | > | CutoffGroup* cg; |
833 | > | |
834 | > | vector<int> GlobalGroupIndices; |
835 | > | |
836 | > | for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
837 | > | |
838 | > | //local index of cutoff group is trivial, it only depends on the |
839 | > | //order of travesing |
840 | > | for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
841 | > | cg = mol->nextCutoffGroup(ci)) { |
842 | > | GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
843 | > | } |
844 | } | |
845 | + | return GlobalGroupIndices; |
846 | + | } |
847 | ||
848 | + | |
849 | + | void SimInfo::prepareTopology() { |
850 | + | int nExclude, nOneTwo, nOneThree, nOneFour; |
851 | + | |
852 | //calculate mass ratio of cutoff group | |
801 | – | vector<RealType> mfact; |
853 | SimInfo::MoleculeIterator mi; | |
854 | Molecule* mol; | |
855 | Molecule::CutoffGroupIterator ci; | |
# | Line 807 | Line 858 | namespace OpenMD { | |
858 | Atom* atom; | |
859 | RealType totalMass; | |
860 | ||
861 | < | //to avoid memory reallocation, reserve enough space for mfact |
862 | < | mfact.reserve(getNCutoffGroups()); |
861 | > | /** |
862 | > | * The mass factor is the relative mass of an atom to the total |
863 | > | * mass of the cutoff group it belongs to. By default, all atoms |
864 | > | * are their own cutoff groups, and therefore have mass factors of |
865 | > | * 1. We need some special handling for massless atoms, which |
866 | > | * will be treated as carrying the entire mass of the cutoff |
867 | > | * group. |
868 | > | */ |
869 | > | massFactors_.clear(); |
870 | > | massFactors_.resize(getNAtoms(), 1.0); |
871 | ||
872 | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { | |
873 | < | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
873 | > | for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
874 | > | cg = mol->nextCutoffGroup(ci)) { |
875 | ||
876 | totalMass = cg->getMass(); | |
877 | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { | |
878 | // Check for massless groups - set mfact to 1 if true | |
879 | < | if (totalMass != 0) |
880 | < | mfact.push_back(atom->getMass()/totalMass); |
879 | > | if (totalMass != 0) |
880 | > | massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
881 | else | |
882 | < | mfact.push_back( 1.0 ); |
882 | > | massFactors_[atom->getLocalIndex()] = 1.0; |
883 | } | |
884 | } | |
885 | } | |
# | Line 833 | Line 893 | namespace OpenMD { | |
893 | identArray_.push_back(atom->getIdent()); | |
894 | } | |
895 | } | |
836 | – | |
837 | – | //fill molMembershipArray |
838 | – | //molMembershipArray is filled by SimCreator |
839 | – | vector<int> molMembershipArray(nGlobalAtoms_); |
840 | – | for (int i = 0; i < nGlobalAtoms_; i++) { |
841 | – | molMembershipArray[i] = globalMolMembership_[i] + 1; |
842 | – | } |
896 | ||
897 | < | //setup fortran simulation |
897 | > | //scan topology |
898 | ||
899 | nExclude = excludedInteractions_.getSize(); | |
900 | nOneTwo = oneTwoInteractions_.getSize(); | |
# | Line 853 | Line 906 | namespace OpenMD { | |
906 | int* oneThreeList = oneThreeInteractions_.getPairList(); | |
907 | int* oneFourList = oneFourInteractions_.getPairList(); | |
908 | ||
909 | < | setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
857 | < | &nExclude, excludeList, |
858 | < | &nOneTwo, oneTwoList, |
859 | < | &nOneThree, oneThreeList, |
860 | < | &nOneFour, oneFourList, |
861 | < | &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
862 | < | &fortranGlobalGroupMembership[0], &isError); |
863 | < | |
864 | < | if( isError ){ |
865 | < | |
866 | < | sprintf( painCave.errMsg, |
867 | < | "There was an error setting the simulation information in fortran.\n" ); |
868 | < | painCave.isFatal = 1; |
869 | < | painCave.severity = OPENMD_ERROR; |
870 | < | simError(); |
871 | < | } |
872 | < | |
873 | < | |
874 | < | sprintf( checkPointMsg, |
875 | < | "succesfully sent the simulation information to fortran.\n"); |
876 | < | |
877 | < | errorCheckPoint(); |
878 | < | |
879 | < | // Setup number of neighbors in neighbor list if present |
880 | < | if (simParams_->haveNeighborListNeighbors()) { |
881 | < | int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
882 | < | setNeighbors(&nlistNeighbors); |
883 | < | } |
884 | < | |
885 | < | #ifdef IS_MPI |
886 | < | //SimInfo is responsible for creating localToGlobalAtomIndex and |
887 | < | //localToGlobalGroupIndex |
888 | < | vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
889 | < | vector<int> localToGlobalCutoffGroupIndex; |
890 | < | mpiSimData parallelData; |
891 | < | |
892 | < | for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
893 | < | |
894 | < | //local index(index in DataStorge) of atom is important |
895 | < | for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
896 | < | localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
897 | < | } |
898 | < | |
899 | < | //local index of cutoff group is trivial, it only depends on the order of travesing |
900 | < | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
901 | < | localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
902 | < | } |
903 | < | |
904 | < | } |
905 | < | |
906 | < | //fill up mpiSimData struct |
907 | < | parallelData.nMolGlobal = getNGlobalMolecules(); |
908 | < | parallelData.nMolLocal = getNMolecules(); |
909 | < | parallelData.nAtomsGlobal = getNGlobalAtoms(); |
910 | < | parallelData.nAtomsLocal = getNAtoms(); |
911 | < | parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
912 | < | parallelData.nGroupsLocal = getNCutoffGroups(); |
913 | < | parallelData.myNode = worldRank; |
914 | < | MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
915 | < | |
916 | < | //pass mpiSimData struct and index arrays to fortran |
917 | < | setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
918 | < | &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
919 | < | &localToGlobalCutoffGroupIndex[0], &isError); |
920 | < | |
921 | < | if (isError) { |
922 | < | sprintf(painCave.errMsg, |
923 | < | "mpiRefresh errror: fortran didn't like something we gave it.\n"); |
924 | < | painCave.isFatal = 1; |
925 | < | simError(); |
926 | < | } |
927 | < | |
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; |
909 | > | topologyDone_ = true; |
910 | } | |
911 | ||
912 | void SimInfo::addProperty(GenericData* genData) { |
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