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"

using namespace std;
namespace OpenMD {

  /**
   * distributeInitialData is essentially a copy of the older fortran 
   * SimulationSetup
   */
  
  void ForceMatrixDecomposition::distributeInitialData() {
    snap_ = sman_->getCurrentSnapshot();
    storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI    
    int nLocal = snap_->getNumberOfAtoms();
    int nGroups = snap_->getNumberOfCutoffGroups();
    
    AtomCommIntRow = new Communicator<Row,int>(nLocal);
    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);

    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);

    cgCommIntRow = new Communicator<Row,int>(nGroups);
    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
    cgCommIntColumn = new Communicator<Column,int>(nGroups);
    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);

    int nAtomsInRow = AtomCommIntRow->getSize();
    int nAtomsInCol = AtomCommIntColumn->getSize();
    int nGroupsInRow = cgCommIntRow->getSize();
    int nGroupsInCol = cgCommIntColumn->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);
    
    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, 
                                      vector<RealType> (nAtomsInRow, 0.0));
    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
                                      vector<RealType> (nAtomsInCol, 0.0));


    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
    
    // gather the information for atomtype IDs (atids):
    vector<int> identsLocal = info_->getIdentArray();
    identsRow.reserve(nAtomsInRow);
    identsCol.reserve(nAtomsInCol);
    
    AtomCommIntRow->gather(identsLocal, identsRow);
    AtomCommIntColumn->gather(identsLocal, identsCol);
    
    AtomLocalToGlobal = info_->getGlobalAtomIndices();
    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
    
    cgLocalToGlobal = info_->getGlobalGroupIndices();
    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);

    // still need:
    // topoDist
    // exclude
#endif
  }
    

  void ForceMatrixDecomposition::distributeData()  {
    snap_ = sman_->getCurrentSnapshot();
    storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI
    
    // gather up the atomic positions
    AtomCommVectorRow->gather(snap_->atomData.position, 
                              atomRowData.position);
    AtomCommVectorColumn->gather(snap_->atomData.position, 
                                 atomColData.position);
    
    // gather up the cutoff group positions
    cgCommVectorRow->gather(snap_->cgData.position, 
                            cgRowData.position);
    cgCommVectorColumn->gather(snap_->cgData.position, 
                               cgColData.position);
    
    // if needed, gather the atomic rotation matrices
    if (storageLayout_ & DataStorage::dslAmat) {
      AtomCommMatrixRow->gather(snap_->atomData.aMat, 
                                atomRowData.aMat);
      AtomCommMatrixColumn->gather(snap_->atomData.aMat, 
                                   atomColData.aMat);
    }
    
    // if needed, gather the atomic eletrostatic frames
    if (storageLayout_ & DataStorage::dslElectroFrame) {
      AtomCommMatrixRow->gather(snap_->atomData.electroFrame, 
                                atomRowData.electroFrame);
      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, 
                                   atomColData.electroFrame);
    }
#endif      
  }
  
  void ForceMatrixDecomposition::collectIntermediateData() {
    snap_ = sman_->getCurrentSnapshot();
    storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI
    
    if (storageLayout_ & DataStorage::dslDensity) {
      
      AtomCommRealRow->scatter(atomRowData.density, 
                               snap_->atomData.density);
      
      int n = snap_->atomData.density.size();
      std::vector<RealType> rho_tmp(n, 0.0);
      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
      for (int i = 0; i < n; i++)
        snap_->atomData.density[i] += rho_tmp[i];
    }
#endif
  }
  
  void ForceMatrixDecomposition::distributeIntermediateData() {
    snap_ = sman_->getCurrentSnapshot();
    storageLayout_ = sman_->getStorageLayout();
#ifdef IS_MPI
    if (storageLayout_ & DataStorage::dslFunctional) {
      AtomCommRealRow->gather(snap_->atomData.functional, 
                              atomRowData.functional);
      AtomCommRealColumn->gather(snap_->atomData.functional, 
                                 atomColData.functional);
    }
    
    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
      AtomCommRealRow->gather(snap_->atomData.functionalDerivative, 
                              atomRowData.functionalDerivative);
      AtomCommRealColumn->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);
    
    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
    for (int i = 0; i < n; i++) {
      snap_->atomData.force[i] += frc_tmp[i];
      frc_tmp[i] = 0.0;
    }
    
    AtomCommVectorColumn->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.force.size();
      vector<Vector3d> trq_tmp(nt, V3Zero);

      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
      for (int i = 0; i < n; i++) {
        snap_->atomData.torque[i] += trq_tmp[i];
        trq_tmp[i] = 0.0;
      }
      
      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
      for (int i = 0; i < n; i++)
        snap_->atomData.torque[i] += trq_tmp[i];
    }
    
    int nLocal = snap_->getNumberOfAtoms();

    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, 
                                       vector<RealType> (nLocal, 0.0));
    
    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
        pot_local[i] += pot_temp[i][ii];
      }
    }
#endif
  }

  
  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
    Vector3d d;
    
#ifdef IS_MPI
    d = cgColData.position[cg2] - cgRowData.position[cg1];
#else
    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
#endif
    
    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;    
  }
    
  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;    
  }

  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
  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    

    InteractionData idat;
#ifdef IS_MPI
    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::dslFunctionalDerivative) {
      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
    }
#else
    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::dslFunctionalDerivative) {
      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
    }
#endif
    
  }
  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
    InteractionData idat;
    skippedCharge1
      skippedCharge2
      rij
      d
    electroMult
    sw
    f
#ifdef IS_MPI

    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]);
    }

    
  }
  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
  }


  /*
   * buildNeighborList
   *
   * first element of pair is row-indexed CutoffGroup
   * second element of pair is column-indexed CutoffGroup
   */
  vector<pair<int, int> >  buildNeighborList() {
    Vector3d dr, invWid, rs, shift;
    Vector3i cc, m1v, m2s;
    RealType rrNebr;
    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;


    vector<pair<int, int> > neighborList;   
    Vector3i nCells;
    Vector3d invWid, r;

    rList_ = (rCut_ + skinThickness_);
    rl2 = rList_ * rList_;

    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_;

    for (i = 0; i < nGroupsInRow; i++) {
      rs = cgRowData.position[i];
      snap_->scaleVector(rs);     
    }
    

    VDiv (invWid, cells, region);
    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
    for (n = 0; n < nMol; n ++) {
      VSAdd (rs, mol[n].r, 0.5, region);
      VMul (cc, rs, invWid);
      c = VLinear (cc, cells) + nMol;
      cellList[n] = cellList[c];
      cellList[c] = n;
    }
    nebrTabLen = 0;
    for (m1z = 0; m1z < cells.z(); m1z++) {
      for (m1y = 0; m1y < cells.y(); m1y++) {
        for (m1x = 0; m1x < cells.x(); m1x++) {
          Vector3i m1v(m1x, m1y, m1z);
          m1 = VLinear(m1v, cells) + nMol;
          for (offset = 0; offset < nOffset_; offset++) {
            m2v = m1v + cellOffsets_[offset];
            shift = V3Zero();

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

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

            m2 = VLinear (m2v, cells) + nMol;
            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
                if (m1 != m2 || j2 < j1) {
                  dr = mol[j1].r - mol[j2].r;
                  VSub (dr, mol[j1].r, mol[j2].r);
                  VVSub (dr, shift);
                  if (VLenSq (dr) < rrNebr) {
                    neighborList.push_back(make_pair(j1, j2));
                  }
                }
              }
            }
          }
        }
      }
    }
  }

  
} //end namespace OpenMD
Revision:	1562
Committed:	Thu May 12 17:00:14 2011 UTC (13 years, 11 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceMatrixDecomposition.cpp*
File size:	16416 byte(s)
Log Message:	changes for cell linked lists
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41	#include "parallel/ForceMatrixDecomposition.hpp"
42	#include "math/SquareMatrix3.hpp"
43	#include "nonbonded/NonBondedInteraction.hpp"
44	#include "brains/SnapshotManager.hpp"
45
46	using namespace std;
47	namespace OpenMD {
48
49	/**
50	* distributeInitialData is essentially a copy of the older fortran
51	* SimulationSetup
52	*/
53
54	void ForceMatrixDecomposition::distributeInitialData() {
55	snap_ = sman_->getCurrentSnapshot();
56	storageLayout_ = sman_->getStorageLayout();
57	#ifdef IS_MPI
58	int nLocal = snap_->getNumberOfAtoms();
59	int nGroups = snap_->getNumberOfCutoffGroups();
60
61	AtomCommIntRow = new Communicator<Row,int>(nLocal);
62	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
65
66	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
67	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
68	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
69	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
70
71	cgCommIntRow = new Communicator<Row,int>(nGroups);
72	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
73	cgCommIntColumn = new Communicator<Column,int>(nGroups);
74	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
75
76	int nAtomsInRow = AtomCommIntRow->getSize();
77	int nAtomsInCol = AtomCommIntColumn->getSize();
78	int nGroupsInRow = cgCommIntRow->getSize();
79	int nGroupsInCol = cgCommIntColumn->getSize();
80
81	// Modify the data storage objects with the correct layouts and sizes:
82	atomRowData.resize(nAtomsInRow);
83	atomRowData.setStorageLayout(storageLayout_);
84	atomColData.resize(nAtomsInCol);
85	atomColData.setStorageLayout(storageLayout_);
86	cgRowData.resize(nGroupsInRow);
87	cgRowData.setStorageLayout(DataStorage::dslPosition);
88	cgColData.resize(nGroupsInCol);
89	cgColData.setStorageLayout(DataStorage::dslPosition);
90
91	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
92	vector<RealType> (nAtomsInRow, 0.0));
93	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94	vector<RealType> (nAtomsInCol, 0.0));
95
96
97	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
98
99	// gather the information for atomtype IDs (atids):
100	vector<int> identsLocal = info_->getIdentArray();
101	identsRow.reserve(nAtomsInRow);
102	identsCol.reserve(nAtomsInCol);
103
104	AtomCommIntRow->gather(identsLocal, identsRow);
105	AtomCommIntColumn->gather(identsLocal, identsCol);
106
107	AtomLocalToGlobal = info_->getGlobalAtomIndices();
108	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110
111	cgLocalToGlobal = info_->getGlobalGroupIndices();
112	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
114
115	// still need:
116	// topoDist
117	// exclude
118	#endif
119	}
120
121
122
123	void ForceMatrixDecomposition::distributeData() {
124	snap_ = sman_->getCurrentSnapshot();
125	storageLayout_ = sman_->getStorageLayout();
126	#ifdef IS_MPI
127
128	// gather up the atomic positions
129	AtomCommVectorRow->gather(snap_->atomData.position,
130	atomRowData.position);
131	AtomCommVectorColumn->gather(snap_->atomData.position,
132	atomColData.position);
133
134	// gather up the cutoff group positions
135	cgCommVectorRow->gather(snap_->cgData.position,
136	cgRowData.position);
137	cgCommVectorColumn->gather(snap_->cgData.position,
138	cgColData.position);
139
140	// if needed, gather the atomic rotation matrices
141	if (storageLayout_ & DataStorage::dslAmat) {
142	AtomCommMatrixRow->gather(snap_->atomData.aMat,
143	atomRowData.aMat);
144	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
145	atomColData.aMat);
146	}
147
148	// if needed, gather the atomic eletrostatic frames
149	if (storageLayout_ & DataStorage::dslElectroFrame) {
150	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
151	atomRowData.electroFrame);
152	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
153	atomColData.electroFrame);
154	}
155	#endif
156	}
157
158	void ForceMatrixDecomposition::collectIntermediateData() {
159	snap_ = sman_->getCurrentSnapshot();
160	storageLayout_ = sman_->getStorageLayout();
161	#ifdef IS_MPI
162
163	if (storageLayout_ & DataStorage::dslDensity) {
164
165	AtomCommRealRow->scatter(atomRowData.density,
166	snap_->atomData.density);
167
168	int n = snap_->atomData.density.size();
169	std::vector<RealType> rho_tmp(n, 0.0);
170	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
171	for (int i = 0; i < n; i++)
172	snap_->atomData.density[i] += rho_tmp[i];
173	}
174	#endif
175	}
176
177	void ForceMatrixDecomposition::distributeIntermediateData() {
178	snap_ = sman_->getCurrentSnapshot();
179	storageLayout_ = sman_->getStorageLayout();
180	#ifdef IS_MPI
181	if (storageLayout_ & DataStorage::dslFunctional) {
182	AtomCommRealRow->gather(snap_->atomData.functional,
183	atomRowData.functional);
184	AtomCommRealColumn->gather(snap_->atomData.functional,
185	atomColData.functional);
186	}
187
188	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
189	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
190	atomRowData.functionalDerivative);
191	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
192	atomColData.functionalDerivative);
193	}
194	#endif
195	}
196
197
198	void ForceMatrixDecomposition::collectData() {
199	snap_ = sman_->getCurrentSnapshot();
200	storageLayout_ = sman_->getStorageLayout();
201	#ifdef IS_MPI
202	int n = snap_->atomData.force.size();
203	vector<Vector3d> frc_tmp(n, V3Zero);
204
205	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
206	for (int i = 0; i < n; i++) {
207	snap_->atomData.force[i] += frc_tmp[i];
208	frc_tmp[i] = 0.0;
209	}
210
211	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
212	for (int i = 0; i < n; i++)
213	snap_->atomData.force[i] += frc_tmp[i];
214
215
216	if (storageLayout_ & DataStorage::dslTorque) {
217
218	int nt = snap_->atomData.force.size();
219	vector<Vector3d> trq_tmp(nt, V3Zero);
220
221	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
222	for (int i = 0; i < n; i++) {
223	snap_->atomData.torque[i] += trq_tmp[i];
224	trq_tmp[i] = 0.0;
225	}
226
227	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
228	for (int i = 0; i < n; i++)
229	snap_->atomData.torque[i] += trq_tmp[i];
230	}
231
232	int nLocal = snap_->getNumberOfAtoms();
233
234	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
235	vector<RealType> (nLocal, 0.0));
236
237	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
238	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
239	for (int ii = 0; ii < pot_temp[i].size(); ii++ ) {
240	pot_local[i] += pot_temp[i][ii];
241	}
242	}
243	#endif
244	}
245
246
247	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
248	Vector3d d;
249
250	#ifdef IS_MPI
251	d = cgColData.position[cg2] - cgRowData.position[cg1];
252	#else
253	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
254	#endif
255
256	snap_->wrapVector(d);
257	return d;
258	}
259
260
261	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
262
263	Vector3d d;
264
265	#ifdef IS_MPI
266	d = cgRowData.position[cg1] - atomRowData.position[atom1];
267	#else
268	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
269	#endif
270
271	snap_->wrapVector(d);
272	return d;
273	}
274
275	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
276	Vector3d d;
277
278	#ifdef IS_MPI
279	d = cgColData.position[cg2] - atomColData.position[atom2];
280	#else
281	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
282	#endif
283
284	snap_->wrapVector(d);
285	return d;
286	}
287
288	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
289	Vector3d d;
290
291	#ifdef IS_MPI
292	d = atomColData.position[atom2] - atomRowData.position[atom1];
293	#else
294	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
295	#endif
296
297	snap_->wrapVector(d);
298	return d;
299	}
300
301	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
302	#ifdef IS_MPI
303	atomRowData.force[atom1] += fg;
304	#else
305	snap_->atomData.force[atom1] += fg;
306	#endif
307	}
308
309	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
310	#ifdef IS_MPI
311	atomColData.force[atom2] += fg;
312	#else
313	snap_->atomData.force[atom2] += fg;
314	#endif
315
316	}
317
318	// filling interaction blocks with pointers
319	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
320
321	InteractionData idat;
322	#ifdef IS_MPI
323	if (storageLayout_ & DataStorage::dslAmat) {
324	idat.A1 = &(atomRowData.aMat[atom1]);
325	idat.A2 = &(atomColData.aMat[atom2]);
326	}
327
328	if (storageLayout_ & DataStorage::dslElectroFrame) {
329	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
330	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
331	}
332
333	if (storageLayout_ & DataStorage::dslTorque) {
334	idat.t1 = &(atomRowData.torque[atom1]);
335	idat.t2 = &(atomColData.torque[atom2]);
336	}
337
338	if (storageLayout_ & DataStorage::dslDensity) {
339	idat.rho1 = &(atomRowData.density[atom1]);
340	idat.rho2 = &(atomColData.density[atom2]);
341	}
342
343	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
344	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
345	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
346	}
347	#else
348	if (storageLayout_ & DataStorage::dslAmat) {
349	idat.A1 = &(snap_->atomData.aMat[atom1]);
350	idat.A2 = &(snap_->atomData.aMat[atom2]);
351	}
352
353	if (storageLayout_ & DataStorage::dslElectroFrame) {
354	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
355	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
356	}
357
358	if (storageLayout_ & DataStorage::dslTorque) {
359	idat.t1 = &(snap_->atomData.torque[atom1]);
360	idat.t2 = &(snap_->atomData.torque[atom2]);
361	}
362
363	if (storageLayout_ & DataStorage::dslDensity) {
364	idat.rho1 = &(snap_->atomData.density[atom1]);
365	idat.rho2 = &(snap_->atomData.density[atom2]);
366	}
367
368	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
369	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
370	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
371	}
372	#endif
373
374	}
375	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
376	InteractionData idat;
377	skippedCharge1
378	skippedCharge2
379	rij
380	d
381	electroMult
382	sw
383	f
384	#ifdef IS_MPI
385
386	if (storageLayout_ & DataStorage::dslElectroFrame) {
387	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
388	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
389	}
390	if (storageLayout_ & DataStorage::dslTorque) {
391	idat.t1 = &(atomRowData.torque[atom1]);
392	idat.t2 = &(atomColData.torque[atom2]);
393	}
394
395
396	}
397	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
398	}
399
400
401	/*
402	* buildNeighborList
403	*
404	* first element of pair is row-indexed CutoffGroup
405	* second element of pair is column-indexed CutoffGroup
406	*/
407	vector<pair<int, int> > buildNeighborList() {
408	Vector3d dr, invWid, rs, shift;
409	Vector3i cc, m1v, m2s;
410	RealType rrNebr;
411	int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
412
413
414	vector<pair<int, int> > neighborList;
415	Vector3i nCells;
416	Vector3d invWid, r;
417
418	rList_ = (rCut_ + skinThickness_);
419	rl2 = rList_ * rList_;
420
421	snap_ = sman_->getCurrentSnapshot();
422	Mat3x3d Hmat = snap_->getHmat();
423	Vector3d Hx = Hmat.getColumn(0);
424	Vector3d Hy = Hmat.getColumn(1);
425	Vector3d Hz = Hmat.getColumn(2);
426
427	nCells.x() = (int) ( Hx.length() )/ rList_;
428	nCells.y() = (int) ( Hy.length() )/ rList_;
429	nCells.z() = (int) ( Hz.length() )/ rList_;
430
431	for (i = 0; i < nGroupsInRow; i++) {
432	rs = cgRowData.position[i];
433	snap_->scaleVector(rs);
434	}
435
436
437	VDiv (invWid, cells, region);
438	for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
439	for (n = 0; n < nMol; n ++) {
440	VSAdd (rs, mol[n].r, 0.5, region);
441	VMul (cc, rs, invWid);
442	c = VLinear (cc, cells) + nMol;
443	cellList[n] = cellList[c];
444	cellList[c] = n;
445	}
446	nebrTabLen = 0;
447	for (m1z = 0; m1z < cells.z(); m1z++) {
448	for (m1y = 0; m1y < cells.y(); m1y++) {
449	for (m1x = 0; m1x < cells.x(); m1x++) {
450	Vector3i m1v(m1x, m1y, m1z);
451	m1 = VLinear(m1v, cells) + nMol;
452	for (offset = 0; offset < nOffset_; offset++) {
453	m2v = m1v + cellOffsets_[offset];
454	shift = V3Zero();
455
456	if (m2v.x() >= cells.x) {
457	m2v.x() = 0;
458	shift.x() = region.x();
459	} else if (m2v.x() < 0) {
460	m2v.x() = cells.x() - 1;
461	shift.x() = - region.x();
462	}
463
464	if (m2v.y() >= cells.y()) {
465	m2v.y() = 0;
466	shift.y() = region.y();
467	} else if (m2v.y() < 0) {
468	m2v.y() = cells.y() - 1;
469	shift.y() = - region.y();
470	}
471
472	m2 = VLinear (m2v, cells) + nMol;
473	for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
474	for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
475	if (m1 != m2 \|\| j2 < j1) {
476	dr = mol[j1].r - mol[j2].r;
477	VSub (dr, mol[j1].r, mol[j2].r);
478	VVSub (dr, shift);
479	if (VLenSq (dr) < rrNebr) {
480	neighborList.push_back(make_pair(j1, j2));
481	}
482	}
483	}
484	}
485	}
486	}
487	}
488	}
489	}
490
491
492	} //end namespace OpenMD