// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
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  // ******************************************************************************
  package ffx.algorithms.optimize.manybody;
  
  import edu.rit.mp.DoubleBuf;
  import edu.rit.pj.Comm;
  import edu.rit.pj.IntegerSchedule;
  import edu.rit.pj.WorkerIntegerForLoop;
  import edu.rit.pj.WorkerRegion;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.Rotamer;
  import ffx.potential.utils.EnergyException;
  
  import java.io.BufferedWriter;
  import java.io.IOException;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.lang.String.format;
  
  /** Compute 2-Body energy values in parallel across nodes. */
  public class TwoBodyEnergyRegion extends WorkerRegion {
  
    private static final Logger logger = Logger.getLogger(TwoBodyEnergyRegion.class.getName());
    private final Residue[] residues;
    private final RotamerOptimization rO;
    private final DistanceMatrix dM;
    private final EnergyExpansion eE;
    private final EliminatedRotamers eR;
    /**
     * A list of all residues being optimized. Note that Box and Window optimizations operate on
     * subsets of this list.
     */
    private final List<Residue> allResiduesList;
    /** Map of self-energy values to compute. */
    private final Map<Integer, Integer[]> twoBodyEnergyMap;
    /** Writes energies to restart file. */
    private final BufferedWriter energyWriter;
    /** World Parallel Java communicator. */
    private final Comm world;
    /** Number of Parallel Java processes. */
    private final int numProc;
    /** Flag to prune clashes. */
    private final boolean prunePairClashes;
    /**
     * If a pair of residues have two atoms closer together than the superposition threshold, the
     * energy is set to NaN.
     */
    private final double superpositionThreshold;
    /** Flag to indicate if this is the master process. */
    private final boolean master;
    /** Rank of this process. */
    private final int rank;
    /** Flag to indicate verbose logging. */
    private final boolean verbose;
    /** If true, write out an energy restart file. */
    private final boolean writeEnergyRestart;
    /**
     * Sets whether files should be printed; true for standalone applications, false for some
     * applications which use rotamer optimization as part of a larger process.
    */
   private final boolean printFiles;
 
   private Set<Integer> keySet;
 
   public TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM,
       EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList,
       BufferedWriter energyWriter, Comm world, int numProc, boolean prunePairClashes,
       double superpositionThreshold, boolean master, int rank, boolean verbose,
       boolean writeEnergyRestart, boolean printFiles) {
     this.rO = rotamerOptimization;
     this.dM = dM;
     this.eE = eE;
     this.eR = eR;
     this.residues = residues;
     this.allResiduesList = allResiduesList;
     this.energyWriter = energyWriter;
     this.world = world;
     this.numProc = numProc;
     this.prunePairClashes = prunePairClashes;
     this.superpositionThreshold = superpositionThreshold;
     this.master = master;
     this.rank = rank;
     this.verbose = verbose;
     this.writeEnergyRestart = writeEnergyRestart;
     this.printFiles = printFiles;
 
     this.twoBodyEnergyMap = eE.getTwoBodyEnergyMap();
     logger.info(format(" Number of 2-body energies to calculate: %d", twoBodyEnergyMap.size()));
   }
 
   @Override
   public void finish() {
     // Pre-Prune if pair-energy is Double.NaN.
     eR.prePrunePairs(residues);
 
     // Prune each rotamer that clashes with all rotamers from a 2nd residue.
     if (prunePairClashes) {
       eR.prunePairClashes(residues);
     }
 
     // Print what we've got so far.
     if (master && verbose) {
       for (int i = 0; i < residues.length; i++) {
         Residue resI = residues[i];
         Rotamer[] rotI = resI.getRotamers();
         for (int ri = 0; ri < rotI.length; ri++) {
           if (eR.check(i, ri)) {
             continue;
           }
           for (int j = i + 1; j < residues.length; j++) {
             Residue resJ = residues[j];
             Rotamer[] rotJ = resJ.getRotamers();
             for (int rj = 0; rj < rotJ.length; rj++) {
               if (eR.check(j, rj) || eR.check(i, ri, j, rj)) {
                 continue;
               }
               logger.info(
                   format(" Pair energy %8s %-2d, %8s %-2d: %s", residues[i].toString(rotI[ri]), ri,
                       residues[j].toString(rotJ[rj]), rj,
                       rO.formatEnergy(eE.get2Body(i, ri, j, rj))));
             }
           }
         }
       }
     }
   }
 
   @Override
   public void run() throws Exception {
     if (!keySet.isEmpty()) {
       execute(0, keySet.size() - 1, new TwoBodyEnergyLoop());
     }
   }
 
   @Override
   public void start() {
     int numPair = twoBodyEnergyMap.size();
     int remainder = numPair % numProc;
 
     // Set padded residue and rotamer to less than zero.
     Integer[] padding = {-1, -1, -1, -1};
 
     int padKey = numPair;
     while (remainder != 0) {
       twoBodyEnergyMap.put(padKey++, padding);
       remainder = twoBodyEnergyMap.size() % numProc;
     }
 
     numPair = twoBodyEnergyMap.size();
     if (numPair % numProc != 0) {
       logger.severe(" Logic error padding pair energies.");
     }
 
     // Load the keySet of pair energies.
     keySet = twoBodyEnergyMap.keySet();
   }
 
   private class TwoBodyEnergyLoop extends WorkerIntegerForLoop {
 
     final DoubleBuf[] resultBuffer;
     final DoubleBuf myBuffer;
 
     TwoBodyEnergyLoop() {
       resultBuffer = new DoubleBuf[numProc];
       for (int i = 0; i < numProc; i++) {
         resultBuffer[i] = DoubleBuf.buffer(new double[5]);
       }
       myBuffer = resultBuffer[rank];
     }
 
     @Override
     public void run(int lb, int ub) {
       for (int key = lb; key <= ub; key++) {
         long time = -System.nanoTime();
         Integer[] job = twoBodyEnergyMap.get(key);
         int i = job[0];
         int ri = job[1];
         int j = job[2];
         int rj = job[3];
 
         myBuffer.put(0, i);
         myBuffer.put(1, ri);
         myBuffer.put(2, j);
         myBuffer.put(3, rj);
         myBuffer.put(4, 0.0);
 
         // Initialize result.
         if (i >= 0 && ri >= 0 && j >= 0 && rj >= 0) {
           if (!eR.check(i, ri) || !eR.check(j, rj) || !eR.check(i, ri, j, rj)) {
             Residue residueI = residues[i];
             Residue residueJ = residues[j];
             Rotamer[] rotI = residues[i].getRotamers();
             Rotamer[] rotJ = residues[j].getRotamers();
             int indexI = allResiduesList.indexOf(residueI);
             int indexJ = allResiduesList.indexOf(residueJ);
             double resDist = dM.getResidueDistance(indexI, ri, indexJ, rj);
             String resDistString = "large";
             if (resDist < Double.MAX_VALUE) {
               resDistString = format("%5.3f", resDist);
             }
 
             double dist = dM.checkDistMatrix(indexI, ri, indexJ, rj);
             String distString = "     large";
             if (dist < Double.MAX_VALUE) {
               distString = format("%10.3f", dist);
             }
 
             double twoBodyEnergy;
             if (dist < superpositionThreshold) {
               // Set the energy to NaN for superposed atoms.
               twoBodyEnergy = Double.NaN;
               logger.info(
                   format(" Pair %8s %-2d, %8s %-2d:\t    NaN at %10.3f A (%s A by res) < %5.3f Ang",
                       residueI.toString(rotI[ri]), ri, residueJ.toString(rotJ[rj]), rj, dist,
                       resDist, superpositionThreshold));
             } else if (dM.checkPairDistThreshold(indexI, ri, indexJ, rj)) {
               // Set the two-body energy to 0.0 for separation distances larger than the two-body cutoff.
               twoBodyEnergy = 0.0;
               time += System.nanoTime();
               logger.info(
                   format(" Pair %8s %-2d, %8s %-2d: %s at %s A (%s A by res) in %6.4f (sec).",
                       residueI.toString(rotI[ri]), ri, residueJ.toString(rotJ[rj]), rj,
                       rO.formatEnergy(twoBodyEnergy), distString, resDistString, time * 1.0e-9));
             } else {
               try {
                 twoBodyEnergy = eE.compute2BodyEnergy(residues, i, ri, j, rj);
                 time += System.nanoTime();
                 logger.info(
                     format(" Pair %8s %-2d, %8s %-2d: %s at %s A (%s A by res) in %6.4f (sec).",
                         residueI.toString(rotI[ri]), ri, residueJ.toString(rotJ[rj]), rj,
                         rO.formatEnergy(twoBodyEnergy), distString, resDistString, time * 1.0e-9));
               } catch (EnergyException ex) {
                 twoBodyEnergy = ex.getEnergy();
                 time += System.nanoTime();
                 logger.info(
                     format(" Pair %8s %-2d, %8s %-2d: %s at %s A (%s A by res) in %6.4f (sec).",
                         residueI.toString(rotI[ri]), ri, residueJ.toString(rotJ[rj]), rj,
                         rO.formatEnergy(twoBodyEnergy), distString, resDistString, time * 1.0e-9));
               }
             }
             myBuffer.put(4, twoBodyEnergy);
           }
         }
 
         // All to All communication
         if (numProc > 1) {
           try {
             world.allGather(myBuffer, resultBuffer);
           } catch (Exception e) {
             logger.log(Level.SEVERE, " Exception communicating pair energies.", e);
           }
         }
 
         // Process the two-body energy received from each process.
         for (DoubleBuf doubleBuf : resultBuffer) {
           int resI = (int) doubleBuf.get(0);
           int rotI = (int) doubleBuf.get(1);
           int resJ = (int) doubleBuf.get(2);
           int rotJ = (int) doubleBuf.get(3);
           double energy = doubleBuf.get(4);
           // Skip for padded result.
           if (resI >= 0 && rotI >= 0 && resJ >= 0 && rotJ >= 0) {
             if (!Double.isFinite(energy)) {
               logger.info(
                   " Rotamer pair eliminated: " + resI + ", " + rotI + ", " + resJ + ", " + rotJ);
               eR.eliminateRotamerPair(residues, resI, rotI, resJ, rotJ, false);
             }
             eE.set2Body(resI, rotI, resJ, rotJ, energy);
             if (rank == 0 && writeEnergyRestart && printFiles) {
               try {
                 energyWriter.append(
                     format("Pair %d %d, %d %d: %16.8f", resI, rotI, resJ, rotJ, energy));
                 energyWriter.newLine();
                 energyWriter.flush();
               } catch (IOException ex) {
                 logger.log(Level.SEVERE, " Exception writing energy restart file.", ex);
               }
             }
           }
         }
       }
     }
 
     @Override
     public IntegerSchedule schedule() {
       // The schedule must be fixed.
       return IntegerSchedule.fixed();
     }
   }
 }