ForceMatrixDecomposition.hpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted 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.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
 
#include "brains/Snapshot.hpp"
#include "math/SquareMatrix3.hpp"
#include "parallel/ForceDecomposition.hpp"
 
#ifdef IS_MPI
#include "parallel/Communicator.hpp"
#endif
 
using namespace std;
namespace OpenMD {
 
  class ForceMatrixDecomposition : public ForceDecomposition {
  public:
    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
    ~ForceMatrixDecomposition();
 
    void distributeInitialData();
    void zeroWorkArrays();
    void distributeData();
    void collectIntermediateData();
    void distributeIntermediateData();
    void collectSelfData();
    void collectData();
 
    // neighbor list routines
    void buildNeighborList(vector<int>& neighborList, vector<int>& point,
                           vector<Vector3d>& savedPositions);
 
    // group bookkeeping
    Vector3d& getGroupVelocityColumn(int cg2);
 
    // Group->atom bookkeeping
    vector<int>& getAtomsInGroupRow(int cg1);
    vector<int>& getAtomsInGroupColumn(int cg2);
    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
    RealType& getMassFactorRow(int atom1);
    RealType& getMassFactorColumn(int atom2);
 
    // spatial data
    Vector3d getIntergroupVector(int cg1, int cg2);
    Vector3d getInteratomicVector(int atom1, int atom2);
 
    // atom bookkeeping
    int& getNAtomsInRow();
    int getTopologicalDistance(int atom1, int atom2);
    vector<int>& getExcludesForAtom(int atom1);
    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
    bool excludeAtomPair(int atom1, int atom2);
    int getGlobalIDRow(int atom1);
    int getGlobalIDCol(int atom1);
    int getGlobalID(int atom1);
    void addForceToAtomRow(int atom1, Vector3d fg);
    void addForceToAtomColumn(int atom2, Vector3d fg);
    Vector3d& getAtomVelocityColumn(int atom2);
 
    // filling interaction blocks with pointers
    void fillInteractionData(InteractionData& idat, int atom1, int atom2,
                             bool newAtom1 = true);
    void unpackInteractionData(InteractionData& idat, int atom1, int atom2);
    void unpackPrePairData(InteractionData& idat, int atom1, int atom2);
 
  private:
    int nLocal_;
    int nGroups_;
    vector<int> AtomLocalToGlobal;
    vector<int> cgLocalToGlobal;
    vector<RealType> groupCutoff;
    vector<int> groupToGtype;
 
#ifdef IS_MPI
    DataStorage atomRowData;
    DataStorage atomColData;
    DataStorage cgRowData;
    DataStorage cgColData;
 
    int nAtomsInRow_;
    int nAtomsInCol_;
    int nGroupsInRow_;
    int nGroupsInCol_;
 
    Communicator<Row> rowComm;
    Communicator<Column> colComm;
 
    Plan<int>* AtomPlanIntRow {nullptr};
    Plan<RealType>* AtomPlanRealRow {nullptr};
    Plan<Vector3d>* AtomPlanVectorRow {nullptr};
    Plan<Mat3x3d>* AtomPlanMatrixRow {nullptr};
    Plan<potVec>* AtomPlanPotRow {nullptr};
 
    Plan<int>* AtomPlanIntColumn {nullptr};
    Plan<RealType>* AtomPlanRealColumn {nullptr};
    Plan<Vector3d>* AtomPlanVectorColumn {nullptr};
    Plan<Mat3x3d>* AtomPlanMatrixColumn {nullptr};
    Plan<potVec>* AtomPlanPotColumn {nullptr};
 
    Plan<int>* cgPlanIntRow {nullptr};
    Plan<Vector3d>* cgPlanVectorRow {nullptr};
    Plan<int>* cgPlanIntColumn {nullptr};
    Plan<Vector3d>* cgPlanVectorColumn {nullptr};
 
    // work arrays for assembling potential energy
    vector<potVec> pot_row;
    vector<potVec> pot_col;
 
    vector<potVec> expot_row;
    vector<potVec> expot_col;
 
    vector<potVec> selepot_row;
    vector<potVec> selepot_col;
 
    vector<int> identsRow;
    vector<int> identsCol;
 
    vector<int> regionsRow;
    vector<int> regionsCol;
 
    vector<AtomType*> atypesRow;
    vector<AtomType*> atypesCol;
 
    vector<int> AtomRowToGlobal;
    vector<int> AtomColToGlobal;
 
  public:
    vector<int> cgRowToGlobal;
    vector<int> cgColToGlobal;
 
  private:
    vector<vector<int>> cellListRow_;
    vector<vector<int>> cellListCol_;
 
    vector<vector<int>> groupListRow_;
    vector<vector<int>> groupListCol_;
 
    vector<RealType> massFactorsRow;
    vector<RealType> massFactorsCol;
 
    vector<int> regionRow;
    vector<int> regionCol;
#endif
  };
}  // namespace OpenMD
 
#endif