src/parallel/ForceMatrixDecomposition.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#include "parallel/ForceMatrixDecomposition.hpp"
#include "math/SquareMatrix3.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "brains/SnapshotManager.hpp"
#include "brains/PairList.hpp"
#include "primitives/Molecule.hpp"

using namespace std;
namespace OpenMD {

ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
        ForceDecomposition(info, iMan) {
        // In a parallel computation, row and colum scans must visit all
        // surrounding cells (not just the 14 upper triangular blocks that
        // are used when the processor can see all pairs)
#ifdef IS_MPI
        cellOffsets_.push_back( Vector3i(-1, 0, 0) );
        cellOffsets_.push_back( Vector3i(-1,-1, 0) );
        cellOffsets_.push_back( Vector3i( 0,-1, 0) );
        cellOffsets_.push_back( Vector3i( 1,-1, 0) );
        cellOffsets_.push_back( Vector3i( 0, 0,-1) );
        cellOffsets_.push_back( Vector3i(-1, 0, 1) );
        cellOffsets_.push_back( Vector3i(-1,-1,-1) );
        cellOffsets_.push_back( Vector3i( 0,-1,-1) );
        cellOffsets_.push_back( Vector3i( 1,-1,-1) );
        cellOffsets_.push_back( Vector3i( 1, 0,-1) );
        cellOffsets_.push_back( Vector3i( 1, 1,-1) );
        cellOffsets_.push_back( Vector3i( 0, 1,-1) );
        cellOffsets_.push_back( Vector3i(-1, 1,-1) );
#endif    
}

/**
 * distributeInitialData is essentially a copy of the older fortran
 * SimulationSetup
 */
void ForceMatrixDecomposition::distributeInitialData() {
        snap_ = sman_->getCurrentSnapshot();
        storageLayout_ = sman_->getStorageLayout();
        ff_ = info_->getForceField();
        nLocal_ = snap_->getNumberOfAtoms();

        nGroups_ = info_->getNLocalCutoffGroups();
        // gather the information for atomtype IDs (atids):
        idents = info_->getIdentArray();
        AtomLocalToGlobal = info_->getGlobalAtomIndices();
        cgLocalToGlobal = info_->getGlobalGroupIndices();
        vector<int> globalGroupMembership = info_->getGlobalGroupMembership();

        massFactors = info_->getMassFactors();

        PairList* excludes = info_->getExcludedInteractions();
        PairList* oneTwo = info_->getOneTwoInteractions();
        PairList* oneThree = info_->getOneThreeInteractions();
        PairList* oneFour = info_->getOneFourInteractions();

#ifdef IS_MPI

        MPI::Intracomm row = rowComm.getComm();
        MPI::Intracomm col = colComm.getComm();

        AtomPlanIntRow = new Plan<int>(row, nLocal_);
        AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
        AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
        AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
        AtomPlanPotRow = new Plan<potVec>(row, nLocal_);

        AtomPlanIntColumn = new Plan<int>(col, nLocal_);
        AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
        AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
        AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
        AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);

        cgPlanIntRow = new Plan<int>(row, nGroups_);
        cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
        cgPlanIntColumn = new Plan<int>(col, nGroups_);
        cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);

        nAtomsInRow_ = AtomPlanIntRow->getSize();
        nAtomsInCol_ = AtomPlanIntColumn->getSize();
        nGroupsInRow_ = cgPlanIntRow->getSize();
        nGroupsInCol_ = cgPlanIntColumn->getSize();

        // Modify the data storage objects with the correct layouts and sizes:
        atomRowData.resize(nAtomsInRow_);
        atomRowData.setStorageLayout(storageLayout_);
        atomColData.resize(nAtomsInCol_);
        atomColData.setStorageLayout(storageLayout_);
        cgRowData.resize(nGroupsInRow_);
        cgRowData.setStorageLayout(DataStorage::dslPosition);
        cgColData.resize(nGroupsInCol_);
        cgColData.setStorageLayout(DataStorage::dslPosition);

        identsRow.resize(nAtomsInRow_);
        identsCol.resize(nAtomsInCol_);

        AtomPlanIntRow->gather(idents, identsRow);
        AtomPlanIntColumn->gather(idents, identsCol);

        // allocate memory for the parallel objects
        atypesRow.resize(nAtomsInRow_);
        atypesCol.resize(nAtomsInCol_);

        for (int i = 0; i < nAtomsInRow_; i++)
        atypesRow[i] = ff_->getAtomType(identsRow[i]);
        for (int i = 0; i < nAtomsInCol_; i++)
        atypesCol[i] = ff_->getAtomType(identsCol[i]);

        pot_row.resize(nAtomsInRow_);
        pot_col.resize(nAtomsInCol_);

        AtomRowToGlobal.resize(nAtomsInRow_);
        AtomColToGlobal.resize(nAtomsInCol_);
        AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
        AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);

        cerr << "Atoms in Local:\n";
        for (int i = 0; i < AtomLocalToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
        }
        cerr << "Atoms in Row:\n";
        for (int i = 0; i < AtomRowToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
        }
        cerr << "Atoms in Col:\n";
        for (int i = 0; i < AtomColToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
        }

        cgRowToGlobal.resize(nGroupsInRow_);
        cgColToGlobal.resize(nGroupsInCol_);
        cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
        cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);

        cerr << "Gruops in Local:\n";
        for (int i = 0; i < cgLocalToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
        }
        cerr << "Groups in Row:\n";
        for (int i = 0; i < cgRowToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
        }
        cerr << "Groups in Col:\n";
        for (int i = 0; i < cgColToGlobal.size(); i++)
        {
                cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
        }

        massFactorsRow.resize(nAtomsInRow_);
        massFactorsCol.resize(nAtomsInCol_);
        AtomPlanRealRow->gather(massFactors, massFactorsRow);
        AtomPlanRealColumn->gather(massFactors, massFactorsCol);

        groupListRow_.clear();
        groupListRow_.resize(nGroupsInRow_);
        for (int i = 0; i < nGroupsInRow_; i++)
        {
                int gid = cgRowToGlobal[i];
                for (int j = 0; j < nAtomsInRow_; j++)
                {
                        int aid = AtomRowToGlobal[j];
                        if (globalGroupMembership[aid] == gid)
                        groupListRow_[i].push_back(j);
                }
        }

        groupListCol_.clear();
        groupListCol_.resize(nGroupsInCol_);
        for (int i = 0; i < nGroupsInCol_; i++)
        {
                int gid = cgColToGlobal[i];
                for (int j = 0; j < nAtomsInCol_; j++)
                {
                        int aid = AtomColToGlobal[j];
                        if (globalGroupMembership[aid] == gid)
                        groupListCol_[i].push_back(j);
                }
        }

        excludesForAtom.clear();
        excludesForAtom.resize(nAtomsInRow_);
        toposForAtom.clear();
        toposForAtom.resize(nAtomsInRow_);
        topoDist.clear();
        topoDist.resize(nAtomsInRow_);
        for (int i = 0; i < nAtomsInRow_; i++)
        {
                int iglob = AtomRowToGlobal[i];

                for (int j = 0; j < nAtomsInCol_; j++)
                {
                        int jglob = AtomColToGlobal[j];

                        if (excludes->hasPair(iglob, jglob))
                        excludesForAtom[i].push_back(j);

                        if (oneTwo->hasPair(iglob, jglob))
                        {
                                toposForAtom[i].push_back(j);
                                topoDist[i].push_back(1);
                        } else
                        {
                                if (oneThree->hasPair(iglob, jglob))
                                {
                                        toposForAtom[i].push_back(j);
                                        topoDist[i].push_back(2);
                                } else
                                {
                                        if (oneFour->hasPair(iglob, jglob))
                                        {
                                                toposForAtom[i].push_back(j);
                                                topoDist[i].push_back(3);
                                        }
                                }
                        }
                }
        }

#endif

        // allocate memory for the parallel objects
        atypesLocal.resize(nLocal_);

        for (int i = 0; i < nLocal_; i++)
                atypesLocal[i] = ff_->getAtomType(idents[i]);

        groupList_.clear();
        groupList_.resize(nGroups_);
        for (int i = 0; i < nGroups_; i++)
        {
                int gid = cgLocalToGlobal[i];
                for (int j = 0; j < nLocal_; j++)
                {
                        int aid = AtomLocalToGlobal[j];
                        if (globalGroupMembership[aid] == gid)
                        {
                                groupList_[i].push_back(j);
                        }
                }
        }

        excludesForAtom.clear();
        excludesForAtom.resize(nLocal_);
        toposForAtom.clear();
        toposForAtom.resize(nLocal_);
        topoDist.clear();
        topoDist.resize(nLocal_);

        for (int i = 0; i < nLocal_; i++)
        {
                int iglob = AtomLocalToGlobal[i];

                for (int j = 0; j < nLocal_; j++)
                {
                        int jglob = AtomLocalToGlobal[j];

                        if (excludes->hasPair(iglob, jglob))
                                excludesForAtom[i].push_back(j);

                        if (oneTwo->hasPair(iglob, jglob))
                        {
                                toposForAtom[i].push_back(j);
                                topoDist[i].push_back(1);
                        } else
                        {
                                if (oneThree->hasPair(iglob, jglob))
                                {
                                        toposForAtom[i].push_back(j);
                                        topoDist[i].push_back(2);
                                } else
                                {
                                        if (oneFour->hasPair(iglob, jglob))
                                        {
                                                toposForAtom[i].push_back(j);
                                                topoDist[i].push_back(3);
                                        }
                                }
                        }
                }
        }

        Globals* simParams_ = info_->getSimParams();
        if (simParams_->haveNeighborListReorderFreq())
        {
                neighborListReorderFreq = simParams_->getNeighborListReorderFreq();
        } else
        {
                neighborListReorderFreq = 0;
        }
        reorderFreqCounter = 1;

        createGtypeCutoffMap();

}

void ForceMatrixDecomposition::createGtypeCutoffMap() {

        RealType tol = 1e-6;
        largestRcut_ = 0.0;
        RealType rc;
        int atid;
        set<AtomType*> atypes = info_->getSimulatedAtomTypes();

        map<int, RealType> atypeCutoff;

        for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at)
        {
                atid = (*at)->getIdent();
                if (userChoseCutoff_)
                        atypeCutoff[atid] = userCutoff_;
                else
                        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
        }

        vector<RealType> gTypeCutoffs;
        // first we do a single loop over the cutoff groups to find the
        // largest cutoff for any atypes present in this group.
#ifdef IS_MPI
        vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
        groupRowToGtype.resize(nGroupsInRow_);
        for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++)
        {
                vector<int> atomListRow = getAtomsInGroupRow(cg1);
                for (vector<int>::iterator ia = atomListRow.begin();
                                ia != atomListRow.end(); ++ia)
                {
                        int atom1 = (*ia);
                        atid = identsRow[atom1];
                        if (atypeCutoff[atid] > groupCutoffRow[cg1])
                        {
                                groupCutoffRow[cg1] = atypeCutoff[atid];
                        }
                }

                bool gTypeFound = false;
                for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
                {
                        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol)
                        {
                                groupRowToGtype[cg1] = gt;
                                gTypeFound = true;
                        }
                }
                if (!gTypeFound)
                {
                        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
                        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
                }

        }
        vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
        groupColToGtype.resize(nGroupsInCol_);
        for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++)
        {
                vector<int> atomListCol = getAtomsInGroupColumn(cg2);
                for (vector<int>::iterator jb = atomListCol.begin();
                                jb != atomListCol.end(); ++jb)
                {
                        int atom2 = (*jb);
                        atid = identsCol[atom2];
                        if (atypeCutoff[atid] > groupCutoffCol[cg2])
                        {
                                groupCutoffCol[cg2] = atypeCutoff[atid];
                        }
                }
                bool gTypeFound = false;
                for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
                {
                        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol)
                        {
                                groupColToGtype[cg2] = gt;
                                gTypeFound = true;
                        }
                }
                if (!gTypeFound)
                {
                        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
                        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
                }
        }
#else

        vector<RealType> groupCutoff(nGroups_, 0.0);
        groupToGtype.resize(nGroups_);
        for (int cg1 = 0; cg1 < nGroups_; cg1++)
        {
                groupCutoff[cg1] = 0.0;
                vector<int> atomList = getAtomsInGroupRow(cg1);
                for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia)
                {
                        int atom1 = (*ia);
                        atid = idents[atom1];
                        if (atypeCutoff[atid] > groupCutoff[cg1])
                                groupCutoff[cg1] = atypeCutoff[atid];
                }

                bool gTypeFound = false;
                for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
                {
                        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol)
                        {
                                groupToGtype[cg1] = gt;
                                gTypeFound = true;
                        }
                }
                if (!gTypeFound)
                {
                        gTypeCutoffs.push_back(groupCutoff[cg1]);
                        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
                }
        }
#endif

        // Now we find the maximum group cutoff value present in the simulation

        RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());

#ifdef IS_MPI
        MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
                        MPI::MAX);
#endif

        RealType tradRcut = groupMax;

        for (int i = 0; i < gTypeCutoffs.size(); i++)
        {
                for (int j = 0; j < gTypeCutoffs.size(); j++)
                {
                        RealType thisRcut;
                        switch (cutoffPolicy_) {
                        case TRADITIONAL:
                                thisRcut = tradRcut;
                                break;
                        case MIX:
                                thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
                                break;
                        case MAX:
                                thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
                                break;
                        default:
                                sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
                                        "hit an unknown cutoff policy!\n");
                                painCave.severity = OPENMD_ERROR;
                                painCave.isFatal = 1;
                                simError();
                                break;
                        }

                        pair<int, int> key = make_pair(i, j);
                        gTypeCutoffMap[key].first = thisRcut;
                        if (thisRcut > largestRcut_)
                                largestRcut_ = thisRcut;
                        gTypeCutoffMap[key].second = thisRcut * thisRcut;
                        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
                        // sanity check

                        if (userChoseCutoff_)
                        {
                                if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001)
                                {
                                        sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
                                                "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
                                        painCave.severity = OPENMD_ERROR;
                                        painCave.isFatal = 1;
                                        simError();
                                }
                        }
                }
        }
}

groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
        int i, j;
#ifdef IS_MPI
        i = groupRowToGtype[cg1];
        j = groupColToGtype[cg2];
#else
        i = groupToGtype[cg1];
        j = groupToGtype[cg2];
#endif    
        return gTypeCutoffMap[make_pair(i, j)];
}

int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
        for (int j = 0; j < toposForAtom[atom1].size(); j++)
        {
                if (toposForAtom[atom1][j] == atom2)
                        return topoDist[atom1][j];
        }
        return 0;
}

void ForceMatrixDecomposition::zeroWorkArrays() {
        pairwisePot = 0.0;
        embeddingPot = 0.0;

#ifdef IS_MPI
        if (storageLayout_ & DataStorage::dslForce)
        {
                fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
                fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
        }

        if (storageLayout_ & DataStorage::dslTorque)
        {
                fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
                fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
        }

        fill(pot_row.begin(), pot_row.end(),
                        Vector<RealType, N_INTERACTION_FAMILIES> (0.0));

        fill(pot_col.begin(), pot_col.end(),
                        Vector<RealType, N_INTERACTION_FAMILIES> (0.0));

        if (storageLayout_ & DataStorage::dslParticlePot)
        {
                fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
                                0.0);
                fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
                                0.0);
        }

        if (storageLayout_ & DataStorage::dslDensity)
        {
                fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
                fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
        }

        if (storageLayout_ & DataStorage::dslFunctional)
        {
                fill(atomRowData.functional.begin(), atomRowData.functional.end(),
                                0.0);
                fill(atomColData.functional.begin(), atomColData.functional.end(),
                                0.0);
        }

        if (storageLayout_ & DataStorage::dslFunctionalDerivative)
        {
                fill(atomRowData.functionalDerivative.begin(),
                                atomRowData.functionalDerivative.end(), 0.0);
                fill(atomColData.functionalDerivative.begin(),
                                atomColData.functionalDerivative.end(), 0.0);
        }

        if (storageLayout_ & DataStorage::dslSkippedCharge)
        {
                fill(atomRowData.skippedCharge.begin(),
                                atomRowData.skippedCharge.end(), 0.0);
                fill(atomColData.skippedCharge.begin(),
                                atomColData.skippedCharge.end(), 0.0);
        }

#endif
        // even in parallel, we need to zero out the local arrays:

        if (storageLayout_ & DataStorage::dslParticlePot)
        {
                fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
        }

        if (storageLayout_ & DataStorage::dslDensity)
        {
                fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0);
        }
        if (storageLayout_ & DataStorage::dslFunctional)
        {
                fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0);
        }
        if (storageLayout_ & DataStorage::dslFunctionalDerivative)
        {
                fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0);
        }
        if (storageLayout_ & DataStorage::dslSkippedCharge)
        {
                fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0);
        }

}

void ForceMatrixDecomposition::distributeData() {
        snap_ = sman_->getCurrentSnapshot();
        storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI

        // gather up the atomic positions
        AtomPlanVectorRow->gather(snap_->atomData.position,
                        atomRowData.position);
        AtomPlanVectorColumn->gather(snap_->atomData.position,
                        atomColData.position);

        // gather up the cutoff group positions

        cerr << "before gather\n";
        for (int i = 0; i < snap_->cgData.position.size(); i++)
        {
                cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
        }

        cgPlanVectorRow->gather(snap_->cgData.position,
                        cgRowData.position);

        cerr << "after gather\n";
        for (int i = 0; i < cgRowData.position.size(); i++)
        {
                cerr << "cgRpos = " << cgRowData.position[i] << "\n";
        }

        cgPlanVectorColumn->gather(snap_->cgData.position,
                        cgColData.position);
        for (int i = 0; i < cgColData.position.size(); i++)
        {
                cerr << "cgCpos = " << cgColData.position[i] << "\n";
        }

        // if needed, gather the atomic rotation matrices
        if (storageLayout_ & DataStorage::dslAmat)
        {
                AtomPlanMatrixRow->gather(snap_->atomData.aMat,
                                atomRowData.aMat);
                AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
                                atomColData.aMat);
        }

        // if needed, gather the atomic eletrostatic frames
        if (storageLayout_ & DataStorage::dslElectroFrame)
        {
                AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
                                atomRowData.electroFrame);
                AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
                                atomColData.electroFrame);
        }

#endif      
}

/* collects information obtained during the pre-pair loop onto local
 * data structures.
 */
void ForceMatrixDecomposition::collectIntermediateData() {
        snap_ = sman_->getCurrentSnapshot();
        storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI

        if (storageLayout_ & DataStorage::dslDensity)
        {

                AtomPlanRealRow->scatter(atomRowData.density,
                                snap_->atomData.density);

                int n = snap_->atomData.density.size();
                vector<RealType> rho_tmp(n, 0.0);
                AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
                for (int i = 0; i < n; i++)
                snap_->atomData.density[i] += rho_tmp[i];
        }
#endif
}

/*
 * redistributes information obtained during the pre-pair loop out to
 * row and column-indexed data structures
 */
void ForceMatrixDecomposition::distributeIntermediateData() {
        snap_ = sman_->getCurrentSnapshot();
        storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI
        if (storageLayout_ & DataStorage::dslFunctional)
        {
                AtomPlanRealRow->gather(snap_->atomData.functional,
                                atomRowData.functional);
                AtomPlanRealColumn->gather(snap_->atomData.functional,
                                atomColData.functional);
        }

        if (storageLayout_ & DataStorage::dslFunctionalDerivative)
        {
                AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
                                atomRowData.functionalDerivative);
                AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
                                atomColData.functionalDerivative);
        }
#endif
}

void ForceMatrixDecomposition::collectData() {
        snap_ = sman_->getCurrentSnapshot();
        storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI    
        int n = snap_->atomData.force.size();
        vector<Vector3d> frc_tmp(n, V3Zero);

        AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
        for (int i = 0; i < n; i++)
        {
                snap_->atomData.force[i] += frc_tmp[i];
                frc_tmp[i] = 0.0;
        }

        AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
        for (int i = 0; i < n; i++)
        {
                snap_->atomData.force[i] += frc_tmp[i];
        }

        if (storageLayout_ & DataStorage::dslTorque)
        {

                int nt = snap_->atomData.torque.size();
                vector<Vector3d> trq_tmp(nt, V3Zero);

                AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
                for (int i = 0; i < nt; i++)
                {
                        snap_->atomData.torque[i] += trq_tmp[i];
                        trq_tmp[i] = 0.0;
                }

                AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
                for (int i = 0; i < nt; i++)
                snap_->atomData.torque[i] += trq_tmp[i];
        }

        if (storageLayout_ & DataStorage::dslSkippedCharge)
        {

                int ns = snap_->atomData.skippedCharge.size();
                vector<RealType> skch_tmp(ns, 0.0);

                AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
                for (int i = 0; i < ns; i++)
                {
                        snap_->atomData.skippedCharge[i] += skch_tmp[i];
                        skch_tmp[i] = 0.0;
                }

                AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
                for (int i = 0; i < ns; i++)
                snap_->atomData.skippedCharge[i] += skch_tmp[i];
        }

        nLocal_ = snap_->getNumberOfAtoms();

        vector<potVec> pot_temp(nLocal_,
                        Vector<RealType, N_INTERACTION_FAMILIES> (0.0));

        // scatter/gather pot_row into the members of my column

        AtomPlanPotRow->scatter(pot_row, pot_temp);

        for (int ii = 0; ii < pot_temp.size(); ii++ )
        pairwisePot += pot_temp[ii];

        fill(pot_temp.begin(), pot_temp.end(),
                        Vector<RealType, N_INTERACTION_FAMILIES> (0.0));

        AtomPlanPotColumn->scatter(pot_col, pot_temp);

        for (int ii = 0; ii < pot_temp.size(); ii++ )
        pairwisePot += pot_temp[ii];
#endif

        //      cerr << "pairwisePot = " << pairwisePot << "\n";
}

int ForceMatrixDecomposition::getNAtomsInRow() {
#ifdef IS_MPI
        return nAtomsInRow_;
#else
        return nLocal_;
#endif
}

/**
 * returns the list of atoms belonging to this group.
 */
vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) {
#ifdef IS_MPI
        return groupListRow_[cg1];
#else 
        return groupList_[cg1];
#endif
}

vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
#ifdef IS_MPI
        return groupListCol_[cg2];
#else 
        return groupList_[cg2];
#endif
}

Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
        Vector3d d;

#ifdef IS_MPI
        d = cgColData.position[cg2] - cgRowData.position[cg1];
        cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
        cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
#else
        d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
        cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
        cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
#endif

        snap_->wrapVector(d);
        return d;
}

Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
        Vector3d d;

        d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
        /*      cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = "
         << snap_->cgData.position[cg1->getLocalIndex()] << "\n";
         cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = "
         << snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/

        snap_->wrapVector(d);
        return d;
}

Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {

        Vector3d d;

#ifdef IS_MPI
        d = cgRowData.position[cg1] - atomRowData.position[atom1];
#else
        d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
#endif

        snap_->wrapVector(d);
        return d;
}

Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
        Vector3d d;

#ifdef IS_MPI
        d = cgColData.position[cg2] - atomColData.position[atom2];
#else
        d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
#endif

        snap_->wrapVector(d);
        return d;
}

RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
#ifdef IS_MPI
        return massFactorsRow[atom1];
#else
        return massFactors[atom1];
#endif
}

RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
#ifdef IS_MPI
        return massFactorsCol[atom2];
#else
        return massFactors[atom2];
#endif

}

Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
        Vector3d d;

#ifdef IS_MPI
        d = atomColData.position[atom2] - atomRowData.position[atom1];
#else
        d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
#endif

        snap_->wrapVector(d);
        return d;
}

vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
        return excludesForAtom[atom1];
}

/**
 * We need to exclude some overcounted interactions that result from
 * the parallel decomposition.
 */
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
        int unique_id_1, unique_id_2;

        //      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
#ifdef IS_MPI
        // in MPI, we have to look up the unique IDs for each atom
        unique_id_1 = AtomRowToGlobal[atom1];
        unique_id_2 = AtomColToGlobal[atom2];

        cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
        // this situation should only arise in MPI simulations
        if (unique_id_1 == unique_id_2) return true;

        // this prevents us from doing the pair on multiple processors
        if (unique_id_1 < unique_id_2)
        {
                if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
        } else
        {
                if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
        }
#endif
        return false;
}

/**
 * We need to handle the interactions for atoms who are involved in
 * the same rigid body as well as some short range interactions
 * (bonds, bends, torsions) differently from other interactions.
 * We'll still visit the pairwise routines, but with a flag that
 * tells those routines to exclude the pair from direct long range
 * interactions.  Some indirect interactions (notably reaction
 * field) must still be handled for these pairs.
 */
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
        int unique_id_2;
#ifdef IS_MPI
        // in MPI, we have to look up the unique IDs for the row atom.
        unique_id_2 = AtomColToGlobal[atom2];
#else
        // in the normal loop, the atom numbers are unique
        unique_id_2 = atom2;
#endif

        for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
        {
                if ((*i) == unique_id_2)
                        return true;
        }

        return false;
}

void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
#ifdef IS_MPI
        atomRowData.force[atom1] += fg;
#else
        snap_->atomData.force[atom1] += fg;
#endif
}

void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
#ifdef IS_MPI
        atomColData.force[atom2] += fg;
#else
        snap_->atomData.force[atom2] += fg;
#endif
}

// filling interaction blocks with pointers
void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {

        idat.excluded = excludeAtomPair(atom1, atom2);

#ifdef IS_MPI
        idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
        //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
        //                         ff_->getAtomType(identsCol[atom2]) );

        if (storageLayout_ & DataStorage::dslAmat)
        {
                idat.A1 = &(atomRowData.aMat[atom1]);
                idat.A2 = &(atomColData.aMat[atom2]);
        }

        if (storageLayout_ & DataStorage::dslElectroFrame)
        {
                idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
                idat.eFrame2 = &(atomColData.electroFrame[atom2]);
        }

        if (storageLayout_ & DataStorage::dslTorque)
        {
                idat.t1 = &(atomRowData.torque[atom1]);
                idat.t2 = &(atomColData.torque[atom2]);
        }

        if (storageLayout_ & DataStorage::dslDensity)
        {
                idat.rho1 = &(atomRowData.density[atom1]);
                idat.rho2 = &(atomColData.density[atom2]);
        }

        if (storageLayout_ & DataStorage::dslFunctional)
        {
                idat.frho1 = &(atomRowData.functional[atom1]);
                idat.frho2 = &(atomColData.functional[atom2]);
        }

        if (storageLayout_ & DataStorage::dslFunctionalDerivative)
        {
                idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
                idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
        }

        if (storageLayout_ & DataStorage::dslParticlePot)
        {
                idat.particlePot1 = &(atomRowData.particlePot[atom1]);
                idat.particlePot2 = &(atomColData.particlePot[atom2]);
        }

        if (storageLayout_ & DataStorage::dslSkippedCharge)
        {
                idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
                idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
        }

#else

        idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
        //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
        //                         ff_->getAtomType(idents[atom2]) );

        if (storageLayout_ & DataStorage::dslAmat)
        {
                idat.A1 = &(snap_->atomData.aMat[atom1]);
                idat.A2 = &(snap_->atomData.aMat[atom2]);
        }

        if (storageLayout_ & DataStorage::dslElectroFrame)
        {
                idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
                idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
        }

        if (storageLayout_ & DataStorage::dslTorque)
        {
                idat.t1 = &(snap_->atomData.torque[atom1]);
                idat.t2 = &(snap_->atomData.torque[atom2]);
        }

        if (storageLayout_ & DataStorage::dslDensity)
        {
                idat.rho1 = &(snap_->atomData.density[atom1]);
                idat.rho2 = &(snap_->atomData.density[atom2]);
        }

        if (storageLayout_ & DataStorage::dslFunctional)
        {
                idat.frho1 = &(snap_->atomData.functional[atom1]);
                idat.frho2 = &(snap_->atomData.functional[atom2]);
        }

        if (storageLayout_ & DataStorage::dslFunctionalDerivative)
        {
                idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
                idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
        }

        if (storageLayout_ & DataStorage::dslParticlePot)
        {
                idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
                idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
        }

        if (storageLayout_ & DataStorage::dslSkippedCharge)
        {
                idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
                idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
        }
#endif
}

void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
#ifdef IS_MPI
        pot_row[atom1] += 0.5 * *(idat.pot);
        pot_col[atom2] += 0.5 * *(idat.pot);

        atomRowData.force[atom1] += *(idat.f1);
        atomColData.force[atom2] -= *(idat.f1);
#else
        pairwisePot += *(idat.pot);

        snap_->atomData.force[atom1] += *(idat.f1);
        snap_->atomData.force[atom2] -= *(idat.f1);
#endif

}

void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
        vector<int> tmp = vector<int> (groupToGtype.size());

        for (int i = 0; i < groupToGtype.size(); ++i)
        {
                tmp[i] = groupToGtype[i];
        }

        for (int i = 0; i < groupToGtype.size(); ++i)
        {
                groupToGtype[i] = tmp[order[i]];
        }
}

void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
        Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
        DataStorage* cgConfig = &(snap_->cgData);
        vector<Vector3d> tmp = vector<Vector3d> (nGroups_);

        for (int i = 0; i < nGroups_; ++i)
        {
                tmp[i] = snap_->cgData.position[i];
        }

        vector<int> mapPos = vector<int> (nGroups_);
        for (int i = 0; i < nGroups_; ++i)
        {
                snap_->cgData.position[i] = tmp[order[i]];
                mapPos[order[i]] = i;
        }

        SimInfo::MoleculeIterator mi;
        Molecule* mol;
        Molecule::CutoffGroupIterator ci;
        CutoffGroup* cg;

        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
        {
                for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
                {
                        cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
                }
        }

        /*      if (info_->getNCutoffGroups() > 0)
         {
         for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
         {
         for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
         {
         printf("gbI:%d locI:%d x:%f y:%f z:%f\n", cg->getGlobalIndex(), cg->getLocalIndex(),
         cgConfig->position[cg->getLocalIndex()].x(), cgConfig->position[cg->getLocalIndex()].y(),
         cgConfig->position[cg->getLocalIndex()].z());
         }
         }
         } else
         {
         // center of mass of the group is the same as position of the atom
         // if cutoff group does not exist
         printf("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
         //                     cgConfig->position = config->position;
         }*/
}

void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
        vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());

        for (int i = 0; i < groupList_.size(); ++i)
        {
                tmp[i] = groupList_[i];
        }

        for (int i = 0; i < groupList_.size(); ++i)
        {
                groupList_[i] = tmp[order[i]];
        }
}

void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
        int n = 0;
        //      printf("Reorder memory time:%f!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
        //                      info_->getSnapshotManager()->getCurrentSnapshot()->getTime());

        /* record the reordered atom indices */
        vector<int> k = vector<int> (nGroups_);

        for (int c = 0; c < H_c_l.size(); ++c)
        {
                for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
                {
                        int i = (*cg)->getGlobalIndex();
                        k[n] = i;
                        ++n;
                }
        }

        //      reorderGroupCutoffs(k);
        //      reorderGroupList(k);
        reorderPosition(k);
}

vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
        //      printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
        // Na = nGroups_
        /* cell occupancy counter */
        //      vector<int> k_c;
        /* c_i - has cell containing atom i (size Na) */
        vector<int> c = vector<int> (nGroups_);
        /* l_i - layer containing atom i (size Na) */
        //      vector<int> l;

        RealType rList_ = (largestRcut_ + skinThickness_);
        Snapshot* snap_ = sman_->getCurrentSnapshot();
        Mat3x3d Hmat = snap_->getHmat();
        Vector3d Hx = Hmat.getColumn(0);
        Vector3d Hy = Hmat.getColumn(1);
        Vector3d Hz = Hmat.getColumn(2);

        nCells_.x() = (int) (Hx.length()) / rList_;
        nCells_.y() = (int) (Hy.length()) / rList_;
        nCells_.z() = (int) (Hz.length()) / rList_;

        Mat3x3d invHmat = snap_->getInvHmat();
        Vector3d rs, scaled, dr;
        Vector3i whichCell;
        int cellIndex;
        int nCtot = nCells_.x() * nCells_.y() * nCells_.z();

        //      k_c = vector<int> (nCtot, 0);

        SimInfo::MoleculeIterator mi;
        Molecule* mol;
        Molecule::CutoffGroupIterator ci;
        CutoffGroup* cg;

        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
        {
                for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
                {
                        rs = snap_->cgData.position[cg->getLocalIndex()];

                        // scaled positions relative to the box vectors
                        scaled = invHmat * rs;

                        // wrap the vector back into the unit box by subtracting integer box
                        // numbers
                        for (int j = 0; j < 3; j++)
                        {
                                scaled[j] -= roundMe(scaled[j]);
                                scaled[j] += 0.5;
                        }

                        // find xyz-indices of cell that cutoffGroup is in.
                        whichCell.x() = nCells_.x() * scaled.x();
                        whichCell.y() = nCells_.y() * scaled.y();
                        whichCell.z() = nCells_.z() * scaled.z();

                        //                      printf("pos x:%f y:%f z:%f cell x:%d y:%d z:%d\n", rs.x(), rs.y(), rs.z(), whichCell.x(), whichCell.y(),
                        //                                      whichCell.z());

                        // find single index of this cell:
                        cellIndex = Vlinear(whichCell, nCells_);

                        c[cg->getGlobalIndex()] = cellIndex;
                }
        }

        //      int k_c_curr;
        //      int k_c_max = 0;
        /* the cell-layer occupancy matrix */
        vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);

        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
        {
                for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))

                {
                        //                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
                        //                      l.push_back(k_c_curr);
                        //
                        //                      /* determines the number of layers in use */
                        //                      if (k_c_max < k_c_curr)
                        //                      {
                        //                              k_c_max = k_c_curr;
                        //                      }
                        H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
                }
        }

        /* Frequency of reordering the memory */
        if (neighborListReorderFreq != 0)
        {
                if (reorderFreqCounter == neighborListReorderFreq)
                {
                        //printf("neighborListReorderFreq:%d\n", neighborListReorderFreq);
                        reorderMemory(H_c_l);
                        reorderFreqCounter = 1;
                } else
                {
                        reorderFreqCounter++;
                }
        }

        int m;
        /* the neighbor matrix */
        vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);

        groupCutoffs cuts;
        CutoffGroup *cg1;

        /* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
        {
                for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
                {
                        /* c' */
                        int c1 = c[cg1->getGlobalIndex()];
                        Vector3i c1v = idxToV(c1, nCells_);

                        /* loops over the neighboring cells c'' */
                        for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
                        {
                                Vector3i c2v = c1v + (*os);

                                if (c2v.x() >= nCells_.x())
                                {
                                        c2v.x() = 0;
                                } else if (c2v.x() < 0)
                                {
                                        c2v.x() = nCells_.x() - 1;
                                }

                                if (c2v.y() >= nCells_.y())
                                {
                                        c2v.y() = 0;
                                } else if (c2v.y() < 0)
                                {
                                        c2v.y() = nCells_.y() - 1;
                                }

                                if (c2v.z() >= nCells_.z())
                                {
                                        c2v.z() = 0;
                                } else if (c2v.z() < 0)
                                {
                                        c2v.z() = nCells_.z() - 1;
                                }

                                int c2 = Vlinear(c2v, nCells_);
                                /* loops over layers l to access the neighbor atoms */
                                for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
                                {
                                        //                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
                                        //                              if(i != *j)
                                        if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
                                        {
                                                dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
                                                snap_->wrapVector(dr);
                                                cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
                                                if (dr.lengthSquare() < cuts.third)
                                                {
                                                        /* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
                                                        neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
                                                }
                                        }
                                }
                        }
                }
        }

        // save the local cutoff group positions for the check that is
        // done on each loop:
        saved_CG_positions_.clear();
        for (int i = 0; i < nGroups_; i++)
                saved_CG_positions_.push_back(snap_->cgData.position[i]);

        return neighborMatW;
}

/*
 * buildNeighborList
 *
 * first element of pair is row-indexed CutoffGroup
 * second element of pair is column-indexed CutoffGroup
 */
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {

        vector<pair<int, int> > neighborList;
        groupCutoffs cuts;
        bool doAllPairs = false;

#ifdef IS_MPI
        cellListRow_.clear();
        cellListCol_.clear();
#else
        cellList_.clear();
#endif

        RealType rList_ = (largestRcut_ + skinThickness_);
        RealType rl2 = rList_ * rList_;
        Snapshot* snap_ = sman_->getCurrentSnapshot();
        Mat3x3d Hmat = snap_->getHmat();
        Vector3d Hx = Hmat.getColumn(0);
        Vector3d Hy = Hmat.getColumn(1);
        Vector3d Hz = Hmat.getColumn(2);

        nCells_.x() = (int) (Hx.length()) / rList_;
        nCells_.y() = (int) (Hy.length()) / rList_;
        nCells_.z() = (int) (Hz.length()) / rList_;

        // handle small boxes where the cell offsets can end up repeating cells

        if (nCells_.x() < 3)
                doAllPairs = true;
        if (nCells_.y() < 3)
                doAllPairs = true;
        if (nCells_.z() < 3)
                doAllPairs = true;

        Mat3x3d invHmat = snap_->getInvHmat();
        Vector3d rs, scaled, dr;
        Vector3i whichCell;
        int cellIndex;
        int nCtot = nCells_.x() * nCells_.y() * nCells_.z();

#ifdef IS_MPI
        cellListRow_.resize(nCtot);
        cellListCol_.resize(nCtot);
#else
        cellList_.resize(nCtot);
#endif

        if (!doAllPairs)
        {
#ifdef IS_MPI

                for (int i = 0; i < nGroupsInRow_; i++)
                {
                        rs = cgRowData.position[i];

                        // scaled positions relative to the box vectors
                        scaled = invHmat * rs;

                        // wrap the vector back into the unit box by subtracting integer box
                        // numbers
                        for (int j = 0; j < 3; j++)
                        {
                                scaled[j] -= roundMe(scaled[j]);
                                scaled[j] += 0.5;
                        }

                        // find xyz-indices of cell that cutoffGroup is in.
                        whichCell.x() = nCells_.x() * scaled.x();
                        whichCell.y() = nCells_.y() * scaled.y();
                        whichCell.z() = nCells_.z() * scaled.z();

                        // find single index of this cell:
                        cellIndex = Vlinear(whichCell, nCells_);

                        // add this cutoff group to the list of groups in this cell;
                        cellListRow_[cellIndex].push_back(i);
                }
                for (int i = 0; i < nGroupsInCol_; i++)
                {
                        rs = cgColData.position[i];

                        // scaled positions relative to the box vectors
                        scaled = invHmat * rs;

                        // wrap the vector back into the unit box by subtracting integer box
                        // numbers
                        for (int j = 0; j < 3; j++)
                        {
                                scaled[j] -= roundMe(scaled[j]);
                                scaled[j] += 0.5;
                        }

                        // find xyz-indices of cell that cutoffGroup is in.
                        whichCell.x() = nCells_.x() * scaled.x();
                        whichCell.y() = nCells_.y() * scaled.y();
                        whichCell.z() = nCells_.z() * scaled.z();

                        // find single index of this cell:
                        cellIndex = Vlinear(whichCell, nCells_);

                        // add this cutoff group to the list of groups in this cell;
                        cellListCol_[cellIndex].push_back(i);
                }
#else
                for (int i = 0; i < nGroups_; i++)
                {
                        rs = snap_->cgData.position[i];

                        // scaled positions relative to the box vectors
                        scaled = invHmat * rs;

                        // wrap the vector back into the unit box by subtracting integer box
                        // numbers
                        for (int j = 0; j < 3; j++)
                        {
                                scaled[j] -= roundMe(scaled[j]);
                                scaled[j] += 0.5;
                        }

                        // find xyz-indices of cell that cutoffGroup is in.
                        whichCell.x() = nCells_.x() * scaled.x();
                        whichCell.y() = nCells_.y() * scaled.y();
                        whichCell.z() = nCells_.z() * scaled.z();

                        // find single index of this cell:
                        cellIndex = Vlinear(whichCell, nCells_);

                        // add this cutoff group to the list of groups in this cell;
                        cellList_[cellIndex].push_back(i);
                }
#endif

                for (int m1z = 0; m1z < nCells_.z(); m1z++)
                {
                        for (int m1y = 0; m1y < nCells_.y(); m1y++)
                        {
                                for (int m1x = 0; m1x < nCells_.x(); m1x++)
                                {
                                        Vector3i m1v(m1x, m1y, m1z);
                                        int m1 = Vlinear(m1v, nCells_);

                                        for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
                                        {

                                                Vector3i m2v = m1v + (*os);

                                                if (m2v.x() >= nCells_.x())
                                                {
                                                        m2v.x() = 0;
                                                } else if (m2v.x() < 0)
                                                {
                                                        m2v.x() = nCells_.x() - 1;
                                                }

                                                if (m2v.y() >= nCells_.y())
                                                {
                                                        m2v.y() = 0;
                                                } else if (m2v.y() < 0)
                                                {
                                                        m2v.y() = nCells_.y() - 1;
                                                }

                                                if (m2v.z() >= nCells_.z())
                                                {
                                                        m2v.z() = 0;
                                                } else if (m2v.z() < 0)
                                                {
                                                        m2v.z() = nCells_.z() - 1;
                                                }

                                                int m2 = Vlinear(m2v, nCells_);

#ifdef IS_MPI
                                                for (vector<int>::iterator j1 = cellListRow_[m1].begin();
                                                                j1 != cellListRow_[m1].end(); ++j1)
                                                {
                                                        for (vector<int>::iterator j2 = cellListCol_[m2].begin();
                                                                        j2 != cellListCol_[m2].end(); ++j2)
                                                        {

                                                                // In parallel, we need to visit *all* pairs of row &
                                                                // column indicies and will truncate later on.
                                                                dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
                                                                snap_->wrapVector(dr);
                                                                cuts = getGroupCutoffs( (*j1), (*j2) );
                                                                if (dr.lengthSquare() < cuts.third)
                                                                {
                                                                        neighborList.push_back(make_pair((*j1), (*j2)));
                                                                }
                                                        }
                                                }
#else

                                                for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
                                                {
                                                        for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
                                                        {

                                                                // Always do this if we're in different cells or if
                                                                // we're in the same cell and the global index of the
                                                                // j2 cutoff group is less than the j1 cutoff group

                                                                if (m2 != m1 || (*j2) < (*j1))
                                                                {
                                                                        dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
                                                                        snap_->wrapVector(dr);
                                                                        cuts = getGroupCutoffs((*j1), (*j2));
                                                                        if (dr.lengthSquare() < cuts.third)
                                                                        {
                                                                                neighborList.push_back(make_pair((*j1), (*j2)));
                                                                        }
                                                                }
                                                        }
                                                }
#endif
                                        }
                                }
                        }
                }
        } else
        {
                // branch to do all cutoff group pairs
#ifdef IS_MPI
                for (int j1 = 0; j1 < nGroupsInRow_; j1++)
                {
                        for (int j2 = 0; j2 < nGroupsInCol_; j2++)
                        {
                                dr = cgColData.position[j2] - cgRowData.position[j1];
                                snap_->wrapVector(dr);
                                cuts = getGroupCutoffs( j1, j2 );
                                if (dr.lengthSquare() < cuts.third)
                                {
                                        neighborList.push_back(make_pair(j1, j2));
                                }
                        }
                }
#else
                for (int j1 = 0; j1 < nGroups_ - 1; j1++)
                {
                        for (int j2 = j1 + 1; j2 < nGroups_; j2++)
                        {
                                dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
                                snap_->wrapVector(dr);
                                cuts = getGroupCutoffs(j1, j2);
                                if (dr.lengthSquare() < cuts.third)
                                {
                                        neighborList.push_back(make_pair(j1, j2));
                                }
                        }
                }
#endif
        }

        // save the local cutoff group positions for the check that is
        // done on each loop:
        saved_CG_positions_.clear();
        for (int i = 0; i < nGroups_; i++)
                saved_CG_positions_.push_back(snap_->cgData.position[i]);

        return neighborList;
}
} //end namespace OpenMD
Revision:	1599
Committed:	Fri Jul 29 19:03:36 2011 UTC (13 years, 9 months ago) by mciznick
File size:	46360 byte(s)
Log Message:	Updated: Build neighbor list method with frequency counter. Additional parameter to md file.