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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 2061 by gezelter, Tue Mar 3 16:24:44 2015 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 513 | Line 513 | namespace OpenMD {
513     * data structures.
514     */
515    void ForceMatrixDecomposition::collectIntermediateData() {
516 + #ifdef IS_MPI
517 +
518      snap_ = sman_->getCurrentSnapshot();
519      storageLayout_ = sman_->getStorageLayout();
520 < #ifdef IS_MPI
519 <    
520 >
521      if (storageLayout_ & DataStorage::dslDensity) {
522        
523        AtomPlanRealRow->scatter(atomRowData.density,
# Line 551 | Line 552 | namespace OpenMD {
552     * row and column-indexed data structures
553     */
554    void ForceMatrixDecomposition::distributeIntermediateData() {
555 + #ifdef IS_MPI
556      snap_ = sman_->getCurrentSnapshot();
557      storageLayout_ = sman_->getStorageLayout();
558 < #ifdef IS_MPI
558 >
559      if (storageLayout_ & DataStorage::dslFunctional) {
560        AtomPlanRealRow->gather(snap_->atomData.functional,
561                                atomRowData.functional);
# Line 572 | Line 574 | namespace OpenMD {
574    
575    
576    void ForceMatrixDecomposition::collectData() {
577 + #ifdef IS_MPI
578      snap_ = sman_->getCurrentSnapshot();
579      storageLayout_ = sman_->getStorageLayout();
580 < #ifdef IS_MPI    
580 >
581      int n = snap_->atomData.force.size();
582      vector<Vector3d> frc_tmp(n, V3Zero);
583      
# Line 683 | Line 686 | namespace OpenMD {
686      AtomPlanPotRow->scatter(pot_row, pot_temp);
687      AtomPlanPotRow->scatter(expot_row, expot_temp);
688  
689 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
689 >    for (std::size_t ii = 0;  ii < pot_temp.size(); ii++ )
690        pairwisePot += pot_temp[ii];
691  
692 <    for (int ii = 0;  ii < expot_temp.size(); ii++ )
692 >    for (std::size_t ii = 0;  ii < expot_temp.size(); ii++ )
693        excludedPot += expot_temp[ii];
694 <        
694 >    
695      if (storageLayout_ & DataStorage::dslParticlePot) {
696        // This is the pairwise contribution to the particle pot.  The
697        // embedding contribution is added in each of the low level
# Line 711 | Line 714 | namespace OpenMD {
714      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
715      AtomPlanPotColumn->scatter(expot_col, expot_temp);    
716      
717 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
717 >    for (std::size_t ii = 0;  ii < pot_temp.size(); ii++ )
718        pairwisePot += pot_temp[ii];    
719  
720 <    for (int ii = 0;  ii < expot_temp.size(); ii++ )
720 >    for (std::size_t ii = 0;  ii < expot_temp.size(); ii++ )
721        excludedPot += expot_temp[ii];    
722 <
722 >    
723      if (storageLayout_ & DataStorage::dslParticlePot) {
724        // This is the pairwise contribution to the particle pot.  The
725        // embedding contribution is added in each of the low level
# Line 782 | Line 785 | namespace OpenMD {
785     * functional) loops onto local data structures.
786     */
787    void ForceMatrixDecomposition::collectSelfData() {
788 +
789 + #ifdef IS_MPI
790      snap_ = sman_->getCurrentSnapshot();
791      storageLayout_ = sman_->getStorageLayout();
792  
788 – #ifdef IS_MPI
793      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
794        RealType ploc1 = embeddingPot[ii];
795        RealType ploc2 = 0.0;
# Line 802 | Line 806 | namespace OpenMD {
806      
807    }
808  
805 –
806 –
809    int& ForceMatrixDecomposition::getNAtomsInRow() {  
810   #ifdef IS_MPI
811      return nAtomsInRow_;
# Line 831 | Line 833 | namespace OpenMD {
833   #endif
834    }
835    
836 <  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
836 >  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
837 >                                                         int cg2){
838 >
839      Vector3d d;
836 –    
840   #ifdef IS_MPI
841      d = cgColData.position[cg2] - cgRowData.position[cg1];
842   #else
# Line 863 | Line 866 | namespace OpenMD {
866    }
867  
868  
869 <  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
870 <
869 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1,
870 >                                                             int cg1) {
871      Vector3d d;
872      
873   #ifdef IS_MPI
# Line 878 | Line 881 | namespace OpenMD {
881      return d;    
882    }
883    
884 <  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
884 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
885 >                                                                int cg2) {
886      Vector3d d;
887      
888   #ifdef IS_MPI
# Line 909 | Line 913 | namespace OpenMD {
913  
914    }
915      
916 <  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
916 >  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
917 >                                                          int atom2){
918      Vector3d d;
919      
920   #ifdef IS_MPI
# Line 931 | Line 936 | namespace OpenMD {
936     * We need to exclude some overcounted interactions that result from
937     * the parallel decomposition.
938     */
939 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
939 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2,
940 >                                              int cg1, int cg2) {
941      int unique_id_1, unique_id_2;
942          
943   #ifdef IS_MPI
# Line 1506 | Line 1512 | namespace OpenMD {
1512          whichCell.y() = nCells_.y() * scaled.y();
1513          whichCell.z() = nCells_.z() * scaled.z();
1514          
1509 –        // find single index of this cell:
1510 –        int m1 = Vlinear(whichCell, nCells_);
1511 –
1515          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1516               os != cellOffsets_.end(); ++os) {
1517                

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