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  • src/parser.cpp

    r29812d rf66195  
    399399 * Sums over "E"-terms to create the "F"-terms
    400400 * \param Matrix MatrixContainer with matrices (LevelCounter by *ColumnCounter) with all the energies.
    401  * \param KeySet KeySetContainer with bond Order and association mapping of each fragment to an order
     401 * \param KeySets KeySetContainer with bond Order and association mapping of each fragment to an order
    402402 * \param Order bond order
    403403 * \return true if summing was successful
    404404 */
    405 bool MatrixContainer::SumSubManyBodyTerms(class MatrixContainer &MatrixValues, class KeySetsContainer &KeySet, int Order)
     405bool MatrixContainer::SumSubManyBodyTerms(class MatrixContainer &MatrixValues, class KeySetsContainer &KeySets, int Order)
    406406{
    407407  // go through each order
    408   for (int CurrentFragment=0;CurrentFragment<KeySet.FragmentsPerOrder[Order];CurrentFragment++) {
    409     //cout << "Current Fragment is " << CurrentFragment << "/" << KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
     408  for (int CurrentFragment=0;CurrentFragment<KeySets.FragmentsPerOrder[Order];CurrentFragment++) {
     409    //cout << "Current Fragment is " << CurrentFragment << "/" << KeySets.OrderSet[Order][CurrentFragment] << "." << endl;
    410410    // then go per order through each suborder and pick together all the terms that contain this fragment
    411411    for(int SubOrder=0;SubOrder<=Order;SubOrder++) { // go through all suborders up to the desired order
    412       for (int j=0;j<KeySet.FragmentsPerOrder[SubOrder];j++) { // go through all possible fragments of size suborder
    413         if (KeySet.Contains(KeySet.OrderSet[Order][CurrentFragment], KeySet.OrderSet[SubOrder][j])) {
    414           //cout << "Current other fragment is " << j << "/" << KeySet.OrderSet[SubOrder][j] << "." << endl;
     412      for (int j=0;j<KeySets.FragmentsPerOrder[SubOrder];j++) { // go through all possible fragments of size suborder
     413        if (KeySets.Contains(KeySets.OrderSet[Order][CurrentFragment], KeySets.OrderSet[SubOrder][j])) {
     414          //cout << "Current other fragment is " << j << "/" << KeySets.OrderSet[SubOrder][j] << "." << endl;
    415415          // if the fragment's indices are all in the current fragment
    416           for(int k=0;k<RowCounter[ KeySet.OrderSet[SubOrder][j] ];k++) { // go through all atoms in this fragment
    417             int m = MatrixValues.Indices[ KeySet.OrderSet[SubOrder][j] ][k];
     416          for(int k=0;k<RowCounter[ KeySets.OrderSet[SubOrder][j] ];k++) { // go through all atoms in this fragment
     417            int m = MatrixValues.Indices[ KeySets.OrderSet[SubOrder][j] ][k];
    418418            //cout << "Current index is " << k << "/" << m << "." << endl;
    419419            if (m != -1) { // if it's not an added hydrogen
    420               for (int l=0;l<RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ];l++) { // look for the corresponding index in the current fragment
    421                 //cout << "Comparing " << m << " with " << MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
    422                 if (m == MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l]) {
     420              for (int l=0;l<RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ];l++) { // look for the corresponding index in the current fragment
     421                //cout << "Comparing " << m << " with " << MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
     422                if (m == MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][l]) {
    423423                  m = l;
    424424                  break;
    … …  
    426426              }
    427427              //cout << "Corresponding index in CurrentFragment is " << m << "." << endl;
    428               if (m > RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ]) {
    429                 cerr << "In fragment No. " << KeySet.OrderSet[Order][CurrentFragment]   << " current force index " << m << " is greater than " << RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     428              if (m > RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
     429                cerr << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current force index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
    430430                return false;
    431431              }
    432432              if (Order == SubOrder) { // equal order is always copy from Energies
    433                 for(int l=ColumnCounter[ KeySet.OrderSet[SubOrder][j] ];l--;) // then adds/subtract each column
    434                   Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][l] += MatrixValues.Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
     433                for(int l=ColumnCounter[ KeySets.OrderSet[SubOrder][j] ];l--;) // then adds/subtract each column
     434                  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][m][l] += MatrixValues.Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l];
    435435              } else {
    436                 for(int l=ColumnCounter[ KeySet.OrderSet[SubOrder][j] ];l--;)
    437                   Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][l] -= Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
     436                for(int l=ColumnCounter[ KeySets.OrderSet[SubOrder][j] ];l--;)
     437                  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][m][l] -= Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l];
    438438              }
    439439            }
    440             //if ((ColumnCounter[ KeySet.OrderSet[SubOrder][j] ]>1) && (RowCounter[0]-1 >= 1))
    441              //cout << "Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
     440            //if ((ColumnCounter[ KeySets.OrderSet[SubOrder][j] ]>1) && (RowCounter[0]-1 >= 1))
     441             //cout << "Fragments[ KeySets.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySets.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
    442442          }
    443443        } else {
    444           //cout << "Fragment " << KeySet.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
     444          //cout << "Fragment " << KeySets.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySets.OrderSet[Order][CurrentFragment] << "." << endl;
    445445        }
    446446      }
    447447    }
    448    //cout << "Final Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << KeySet.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][KeySet.AtomCounter[0]-1][1] << endl;
     448   //cout << "Final Fragments[ KeySets.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySets.OrderSet[Order][CurrentFragment] << " ][" << KeySets.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][KeySets.AtomCounter[0]-1][1] << endl;
    449449  }
    450450
    … …  
    534534 * \param Matrix MatrixContainer with matrices (LevelCounter by *ColumnCounter) with all the energies.
    535535 * \param CorrectionFragments MatrixContainer with hydrogen saturation correction per fragments
    536  * \param KeySet KeySetContainer with bond Order and association mapping of each fragment to an order
     536 * \param KeySets KeySetContainer with bond Order and association mapping of each fragment to an order
    537537 * \param Order bond order
    538538 * \parsm sign +1 or -1
    539539 * \return true if summing was successful
    540540 */
    541 bool EnergyMatrix::SumSubEnergy(class EnergyMatrix &Fragments, class EnergyMatrix *CorrectionFragments, class KeySetsContainer &KeySet, int Order, double sign)
     541bool EnergyMatrix::SumSubEnergy(class EnergyMatrix &Fragments, class EnergyMatrix *CorrectionFragments, class KeySetsContainer &KeySets, int Order, double sign)
    542542{
    543543  // sum energy
    544544  if (CorrectionFragments == NULL)
    545     for(int i=KeySet.FragmentsPerOrder[Order];i--;)
    546       for(int j=RowCounter[ KeySet.OrderSet[Order][i] ];j--;)
    547         for(int k=ColumnCounter[ KeySet.OrderSet[Order][i] ];k--;)
    548           Matrix[MatrixCounter][j][k] += sign*Fragments.Matrix[ KeySet.OrderSet[Order][i] ][j][k];
     545    for(int i=KeySets.FragmentsPerOrder[Order];i--;)
     546      for(int j=RowCounter[ KeySets.OrderSet[Order][i] ];j--;)
     547        for(int k=ColumnCounter[ KeySets.OrderSet[Order][i] ];k--;)
     548          Matrix[MatrixCounter][j][k] += sign*Fragments.Matrix[ KeySets.OrderSet[Order][i] ][j][k];
    549549  else
    550     for(int i=KeySet.FragmentsPerOrder[Order];i--;)
    551       for(int j=RowCounter[ KeySet.OrderSet[Order][i] ];j--;)
    552         for(int k=ColumnCounter[ KeySet.OrderSet[Order][i] ];k--;)
    553           Matrix[MatrixCounter][j][k] += sign*(Fragments.Matrix[ KeySet.OrderSet[Order][i] ][j][k] + CorrectionFragments->Matrix[ KeySet.OrderSet[Order][i] ][j][k]);
     550    for(int i=KeySets.FragmentsPerOrder[Order];i--;)
     551      for(int j=RowCounter[ KeySets.OrderSet[Order][i] ];j--;)
     552        for(int k=ColumnCounter[ KeySets.OrderSet[Order][i] ];k--;)
     553          Matrix[MatrixCounter][j][k] += sign*(Fragments.Matrix[ KeySets.OrderSet[Order][i] ][j][k] + CorrectionFragments->Matrix[ KeySets.OrderSet[Order][i] ][j][k]);
    554554  return true;
    555555};
    … …  
    641641/** Sums the forces and puts into last element of \a ForceMatrix::Matrix.
    642642 * \param Matrix MatrixContainer with matrices (LevelCounter by *ColumnCounter) with all the energies.
    643  * \param KeySet KeySetContainer with bond Order and association mapping of each fragment to an order
     643 * \param KeySets KeySetContainer with bond Order and association mapping of each fragment to an order
    644644 * \param Order bond order
    645645 *  \param sign +1 or -1
    646646 * \return true if summing was successful
    647647 */
    648 bool ForceMatrix::SumSubForces(class ForceMatrix &Fragments, class KeySetsContainer &KeySet, int Order, double sign)
     648bool ForceMatrix::SumSubForces(class ForceMatrix &Fragments, class KeySetsContainer &KeySets, int Order, double sign)
    649649{
    650650  int FragmentNr;
    651651  // sum forces
    652   for(int i=0;i<KeySet.FragmentsPerOrder[Order];i++) {
    653     FragmentNr = KeySet.OrderSet[Order][i];
     652  for(int i=0;i<KeySets.FragmentsPerOrder[Order];i++) {
     653    FragmentNr = KeySets.OrderSet[Order][i];
    654654    for(int l=0;l<RowCounter[ FragmentNr ];l++) {
    655655      int j = Indices[ FragmentNr ][l];
    … …  
    778778/** Sums the hessian entries and puts into last element of \a HessianMatrix::Matrix.
    779779 * \param Matrix MatrixContainer with matrices (LevelCounter by *ColumnCounter) with all the energies.
    780  * \param KeySet KeySetContainer with bond Order and association mapping of each fragment to an order
     780 * \param KeySets KeySetContainer with bond Order and association mapping of each fragment to an order
    781781 * \param Order bond order
    782782 *  \param sign +1 or -1
    783783 * \return true if summing was successful
    784784 */
    785 bool HessianMatrix::SumSubHessians(class HessianMatrix &Fragments, class KeySetsContainer &KeySet, int Order, double sign)
     785bool HessianMatrix::SumSubHessians(class HessianMatrix &Fragments, class KeySetsContainer &KeySets, int Order, double sign)
    786786{
    787787  int FragmentNr;
    788788  // sum forces
    789   for(int i=0;i<KeySet.FragmentsPerOrder[Order];i++) {
    790     FragmentNr = KeySet.OrderSet[Order][i];
     789  for(int i=0;i<KeySets.FragmentsPerOrder[Order];i++) {
     790    FragmentNr = KeySets.OrderSet[Order][i];
    791791    for(int l=0;l<RowCounter[ FragmentNr ];l++) {
    792792      int j = Indices[ FragmentNr ][l];
    … …  
    823823 * Sums over "E"-terms to create the "F"-terms
    824824 * \param Matrix MatrixContainer with matrices (LevelCounter by *ColumnCounter) with all the energies.
    825  * \param KeySet KeySetContainer with bond Order and association mapping of each fragment to an order
     825 * \param KeySets KeySetContainer with bond Order and association mapping of each fragment to an order
    826826 * \param Order bond order
    827827 * \return true if summing was successful
    828828 */
    829 bool HessianMatrix::SumSubManyBodyTerms(class MatrixContainer &MatrixValues, class KeySetsContainer &KeySet, int Order)
     829bool HessianMatrix::SumSubManyBodyTerms(class MatrixContainer &MatrixValues, class KeySetsContainer &KeySets, int Order)
    830830{
    831831  // go through each order
    832   for (int CurrentFragment=0;CurrentFragment<KeySet.FragmentsPerOrder[Order];CurrentFragment++) {
    833     //cout << "Current Fragment is " << CurrentFragment << "/" << KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
     832  for (int CurrentFragment=0;CurrentFragment<KeySets.FragmentsPerOrder[Order];CurrentFragment++) {
     833    //cout << "Current Fragment is " << CurrentFragment << "/" << KeySets.OrderSet[Order][CurrentFragment] << "." << endl;
    834834    // then go per order through each suborder and pick together all the terms that contain this fragment
    835835    for(int SubOrder=0;SubOrder<=Order;SubOrder++) { // go through all suborders up to the desired order
    836       for (int j=0;j<KeySet.FragmentsPerOrder[SubOrder];j++) { // go through all possible fragments of size suborder
    837         if (KeySet.Contains(KeySet.OrderSet[Order][CurrentFragment], KeySet.OrderSet[SubOrder][j])) {
    838           //cout << "Current other fragment is " << j << "/" << KeySet.OrderSet[SubOrder][j] << "." << endl;
     836      for (int j=0;j<KeySets.FragmentsPerOrder[SubOrder];j++) { // go through all possible fragments of size suborder
     837        if (KeySets.Contains(KeySets.OrderSet[Order][CurrentFragment], KeySets.OrderSet[SubOrder][j])) {
     838          //cout << "Current other fragment is " << j << "/" << KeySets.OrderSet[SubOrder][j] << "." << endl;
    839839          // if the fragment's indices are all in the current fragment
    840           for(int k=0;k<RowCounter[ KeySet.OrderSet[SubOrder][j] ];k++) { // go through all atoms in this fragment
    841             int m = MatrixValues.Indices[ KeySet.OrderSet[SubOrder][j] ][k];
     840          for(int k=0;k<RowCounter[ KeySets.OrderSet[SubOrder][j] ];k++) { // go through all atoms in this fragment
     841            int m = MatrixValues.Indices[ KeySets.OrderSet[SubOrder][j] ][k];
    842842            //cout << "Current row index is " << k << "/" << m << "." << endl;
    843843            if (m != -1) { // if it's not an added hydrogen
    844               for (int l=0;l<RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ];l++) { // look for the corresponding index in the current fragment
    845                 //cout << "Comparing " << m << " with " << MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
    846                 if (m == MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l]) {
     844              for (int l=0;l<RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ];l++) { // look for the corresponding index in the current fragment
     845                //cout << "Comparing " << m << " with " << MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
     846                if (m == MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][l]) {
    847847                  m = l;
    848848                  break; 
    … …  
    850850              }
    851851              //cout << "Corresponding row index for " << k << " in CurrentFragment is " << m << "." << endl;
    852               if (m > RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ]) {
    853                 cerr << "In fragment No. " << KeySet.OrderSet[Order][CurrentFragment]   << " current row index " << m << " is greater than " << RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     852              if (m > RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
     853                cerr << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current row index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
    854854                return false;
    855855              }
    856856             
    857               for(int l=0;l<ColumnCounter[ KeySet.OrderSet[SubOrder][j] ];l++) {
    858                 int n = MatrixValues.Indices[ KeySet.OrderSet[SubOrder][j] ][l];
     857              for(int l=0;l<ColumnCounter[ KeySets.OrderSet[SubOrder][j] ];l++) {
     858                int n = MatrixValues.Indices[ KeySets.OrderSet[SubOrder][j] ][l];
    859859                //cout << "Current column index is " << l << "/" << n << "." << endl;
    860860                if (n != -1) { // if it's not an added hydrogen
    861                   for (int p=0;p<ColumnCounter[ KeySet.OrderSet[Order][CurrentFragment] ];p++) { // look for the corresponding index in the current fragment
    862                     //cout << "Comparing " << n << " with " << MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][p] << "." << endl;
    863                     if (n == MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][p]) {
     861                  for (int p=0;p<ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ];p++) { // look for the corresponding index in the current fragment
     862                    //cout << "Comparing " << n << " with " << MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][p] << "." << endl;
     863                    if (n == MatrixValues.Indices[ KeySets.OrderSet[Order][CurrentFragment] ][p]) {
    864864                      n = p;
    865865                      break; 
    … …  
    867867                  }
    868868                  //cout << "Corresponding column index for " << l << " in CurrentFragment is " << n << "." << endl;
    869                   if (n > ColumnCounter[ KeySet.OrderSet[Order][CurrentFragment] ]) {
    870                     cerr << "In fragment No. " << KeySet.OrderSet[Order][CurrentFragment]   << " current column index " << n << " is greater than " << ColumnCounter[ KeySet.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     869                  if (n > ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
     870                    cerr << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current column index " << n << " is greater than " << ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
    871871                    return false;
    872872                  }
    873873                  if (Order == SubOrder) { // equal order is always copy from Energies
    874                     //cout << "Adding " << MatrixValues.Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l] << " from [" << k << "][" << l << "] onto [" << m << "][" << n << "]." << endl;
    875                     Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][n] += MatrixValues.Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
     874                    //cout << "Adding " << MatrixValues.Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l] << " from [" << k << "][" << l << "] onto [" << m << "][" << n << "]." << endl;
     875                    Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][m][n] += MatrixValues.Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l];
    876876                  } else {
    877                     //cout << "Subtracting " << Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l] << " from [" << k << "][" << l << "] onto [" << m << "][" << n << "]." << endl;
    878                     Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][m][n] -= Matrix[ KeySet.OrderSet[SubOrder][j] ][k][l];
     877                    //cout << "Subtracting " << Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l] << " from [" << k << "][" << l << "] onto [" << m << "][" << n << "]." << endl;
     878                    Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][m][n] -= Matrix[ KeySets.OrderSet[SubOrder][j] ][k][l];
    879879                  }
    880880                }
    881881              }
    882882            }
    883             //if ((ColumnCounter[ KeySet.OrderSet[SubOrder][j] ]>1) && (RowCounter[0]-1 >= 1))
    884              //cout << "Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
     883            //if ((ColumnCounter[ KeySets.OrderSet[SubOrder][j] ]>1) && (RowCounter[0]-1 >= 1))
     884             //cout << "Fragments[ KeySets.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySets.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
    885885          }
    886886        } else {
    887           //cout << "Fragment " << KeySet.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
     887          //cout << "Fragment " << KeySets.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySets.OrderSet[Order][CurrentFragment] << "." << endl;
    888888        }
    889889      }
    890890    }
    891    //cout << "Final Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << KeySet.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][KeySet.AtomCounter[0]-1][1] << endl;
     891   //cout << "Final Fragments[ KeySets.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySets.OrderSet[Order][CurrentFragment] << " ][" << KeySets.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySets.OrderSet[Order][CurrentFragment] ][KeySets.AtomCounter[0]-1][1] << endl;
    892892  }
    893893 
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