//******************************************************************************
   //
   // 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.
  //
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  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
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  // 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
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  // permission to link this library with independent modules to produce an
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  //******************************************************************************
  package ffx.algorithms.commands;
  
  import ffx.algorithms.ParallelStateEnergy;
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.crystal.Crystal;
  import ffx.crystal.CrystalPotential;
  import ffx.numerics.Potential;
  import ffx.numerics.estimator.FreeEnergyDifferenceReporter;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.cli.AlchemicalOptions;
  import ffx.potential.cli.TopologyOptions;
  import ffx.potential.parsers.BARFilter;
  import ffx.potential.parsers.SystemFilter;
  import ffx.utilities.FFXBinding;
  import org.apache.commons.configuration2.Configuration;
  import org.apache.commons.io.FilenameUtils;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.io.IOException;
  import java.nio.file.Files;
  import java.nio.file.Path;
  import java.nio.file.Paths;
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.List;
  import java.util.regex.Matcher;
  import java.util.regex.Pattern;
  import java.util.stream.Stream;
  
  import static java.lang.String.format;
  
  /**
   * The BAR script finds the free energy difference across a lambda window. It presently assumes
   * that the number of files composing the first end of the window equals the number of files
   * composing the other end.
   * <br>
   * Usage:
   * <br>
   * ffxc BAR [options] &lt;structures1&gt; &lt;structures2&gt;
   */
  @Command(description = " Evaluates a free energy change with the Bennett Acceptance Ratio algorithm using pregenerated snapshots.", name = "BAR")
  public class BAR extends AlgorithmsCommand {
  
    @Mixin
    private AlchemicalOptions alchemicalOptions;
  
    @Mixin
    private TopologyOptions topologyOptions;
  
    /**
     * --eb or --evaluateBARFiles Read in Tinker BAR files and evaluate the free energy difference.
     */
    @Option(names = {"--eb", "--evaluateBAR"}, paramLabel = "false", defaultValue = "false",
        description = "Evaluate Free Energy Differences from Tinker BAR files.")
    private boolean evaluateBARFiles = false;
  
    @Option(names = {"--l2", "--lambdaTwo"}, paramLabel = "1.0",
       description = "Lambda value for the upper edge of the window")
   private double lambda2 = 1.0;
 
   @Option(names = {"-t", "--temperature"}, paramLabel = "298.15",
       description = "Temperature for system")
   private double temperature = 298.15;
 
   @Option(names = {"--dV", "--volume"}, paramLabel = "false",
       description = "Write out snapshot volumes to the Tinker BAR file.")
   private boolean includeVolume = false;
 
   @Option(names = {"--ns", "--nStates"}, paramLabel = "2",
       description = "If not equal to two, auto-determine lambda values and subdirectories (overrides other flags).")
   private int nStates = 2;
 
   @Option(names = {"--sa", "--sortedArc"}, paramLabel = "false",
       description = "If set, use sorted archive values.")
   private boolean sortedArc = false;
 
   @Option(names = {"--ss", "--startSnapshot"}, paramLabel = "0",
       description = "Start at this snapshot when reading in Tinker BAR files (indexed from 0).")
   private int startingSnapshot = 0;
 
   @Option(names = {"--es", "--endSnapshot"}, paramLabel = "0",
       description = "End at this snapshot when reading in Tinker BAR files (indexed from 0).")
   private int endingSnapshot = 0;
 
   /**
    * --ni or --nIterations Maximum number of allowable iterations for BAR calculation.
    */
   @Option(names = {"--ni", "--nIterations"}, paramLabel = "1000",
       description = "Specify the maximum number of iterations for BAR convergence.")
   private int nIterations = 1000;
 
   /**
    * -e or --eps Convergence criterion for BAR iteration.
    */
   @Option(names = {"-e", "--eps"}, paramLabel = "1.0E-4",
       description = "Specify convergence cutoff for BAR calculation.")
   private double eps = 1.0E-4;
 
   /**
    * The final argument(s) can be filenames for lambda windows in order.
    */
   @Parameters(arity = "0..*", paramLabel = "files",
       description = "A single PDB/XYZ when windows are auto-determined (or two for dual topology). Two trajectory files for BAR between two ensembles (or four for dual topology).")
   private List<String> filenames = null;
 
   /**
    * Additional properties.
    */
   private Configuration additionalProperties;
 
   /**
    * Molecular assemblies to compute energies.
    */
   MolecularAssembly[] topologies;
 
   /**
    * Number of Topologies.
    */
   private int numTopologies;
 
   /**
    * Potential object for the crystal.
    */
   CrystalPotential potential;
 
   /**
    * Number of input files.
    */
   int nFiles;
 
   /**
    * Input files for BAR.
    */
   private String[] files;
 
   /**
    * Lambda values for each state.
    */
   double[] lambdaValues;
 
   /**
    * Compute and log out the free energy differences.
    */
   private FreeEnergyDifferenceReporter reporter;
 
   /**
    * BAR Constructor.
    */
   public BAR() {
     super();
   }
 
   /**
    * BAR Constructor.
    *
    * @param binding The Binding to use.
    */
   public BAR(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * BAR constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public BAR(String[] args) {
     super(args);
   }
 
   /**
    * Sets an optional Configuration with additional properties.
    *
    * @param additionalProps Additional properties configuration.
    */
   public void setProperties(Configuration additionalProps) {
     this.additionalProperties = additionalProps;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public BAR run() {
     // Initialize the script.
     if (!init()) {
       return this;
     }
 
     /**
      * Load user supplied files into an array.
      */
     if (filenames == null) {
       nFiles = 0;
       files = null;
     } else {
       nFiles = filenames.size();
       files = new String[nFiles];
       for (int i = 0; i < nFiles; i++) {
         files[i] = filenames.get(i);
       }
     }
 
     // Evaluate free energy differences from BAR files.
     if (evaluateBARFiles) {
       // 1) Define the number of states and concordant BAR files (windows = states - 1).
       // 2) Read in the energy and volume data from BAR files.
       // 3) Compute the free energy differences.
       if (nFiles == 0) {
         logger.info(" Please supply a BAR file or directory to be evaluated.");
         return this;
       }
 
       BARFilter[] barFilters = null;
       if (nStates == 2 && nFiles == 1) {
         // If the number of states is 2, evaluate a single BAR file.
         logger.info(format(" Evaluating a single BAR file: %s.", files[0]));
         barFilters = new BARFilter[1];
         barFilters[0] = new BARFilter(new File(files[0]), startingSnapshot, endingSnapshot);
         // Define the lambda values.
         lambdaValues = new double[2];
         lambdaValues[0] = alchemicalOptions.getInitialLambda();
         lambdaValues[1] = lambda2;
       } else if (nStates > 2 && nFiles == 1) {
         // If the number of states is greater than 2, evaluate multiple BAR files from a directory.
         logger.info(format(" Evaluating BAR files from directory %s.", files[0]));
         // Auto-determine bar files from the "bar" subdirectory.
         logger.info(" Auto-detecting BAR files and lambda values.");
         Path subdirectoryPath = Paths.get(files[0]);
         // Regular expression to match files with the form "filename_XX.bar"
         Pattern pattern = Pattern.compile(".*_(\\d+)\\.bar");
         // List to hold file paths
         List<String> fileList = new ArrayList<>();
         try (Stream<Path> paths = Files.list(subdirectoryPath)) {
           paths.filter(Files::isRegularFile)
               .filter(path -> {
                 Matcher matcher = pattern.matcher(path.getFileName().toString());
                 return matcher.matches();
               })
               .sorted(Comparator.comparingInt(path -> {
                 Matcher matcher = pattern.matcher(path.getFileName().toString());
                 matcher.matches();
                 return Integer.parseInt(matcher.group(1));
               }))
               .forEach(path -> fileList.add(path.toString()));
         } catch (IOException e) {
           logger.info(" Error reading files from a directory.\n" + e.toString());
           e.printStackTrace();
           return this;
         }
 
         int numFiles = fileList.size();
         if (numFiles != nStates - 1) {
           logger.info(format(" The number of bar files (%d) does not concord with the number of states (%d).", numFiles, nStates));
           return this;
         }
 
         // Define the lambda values.
         lambdaValues = new double[nStates];
         for (int l = 0; l < nStates; l++) {
           lambdaValues[l] = alchemicalOptions.getInitialLambda(nStates, l, true);
         }
         barFilters = new BARFilter[numFiles];
         for (int i = 0; i < numFiles; i++) {
           String filename = fileList.get(i);
           File barFile = new File(filename);
           barFilters[i] = new BARFilter(barFile, startingSnapshot, endingSnapshot);
           logger.info(format(" Window L=%6.4f to L=%6.4f from %s",
               lambdaValues[i], lambdaValues[i + 1], filename));
         }
       }
 
       // Allocate space for energy and volume arrays.
       double[][] energiesLow = new double[nStates][];
       double[][] energiesAt = new double[nStates][];
       double[][] energiesHigh = new double[nStates][];
       double[][] volume = new double[nStates][];
       double[] temperatures = new double[nStates];
 
       // Load BAR files.
       readBARFiles(barFilters, energiesLow, energiesAt, energiesHigh, volume, temperatures);
 
       // Compute free energy differences.
       reporter = new FreeEnergyDifferenceReporter(nStates, lambdaValues, temperatures, eps, nIterations,
           energiesLow, energiesAt, energiesHigh, volume);
       reporter.report();
 
       // Exit the script.
       return this;
     }
 
     // Create BAR files for later evaluation of free energy differences.
     logger.info(" Writing BAR files.");
 
     numTopologies = 1;
     if (nFiles <= 1 && nStates < 2) {
       logger.info(" At least two states must be specified");
       return this;
     } else if (nFiles == 1 && nStates >= 2) {
       logger.info(format(" Auto-detecting %d states for single topology:\n %s.", nStates, files[0]));
     } else if (nFiles == 2 && nStates >= 2) {
       logger.info(format(" Auto-detecting %d states for dual topology:\n %s\n %s.", nStates, files[0], files[1]));
       numTopologies = 2;
     } else if (nFiles == 2) {
       logger.info(format(" Applying BAR between two single topology ensembles:\n %s\n %s.", files[0], files[1]));
       nStates = 2;
     } else if (nFiles == 4) {
       logger.info(format(" Applying BAR between two dual topology ensembles:\n %s %s\n %s %s.",
           files[0], files[1], files[2], files[3]));
       numTopologies = 2;
       nStates = 2;
     } else {
       logger.info(format(" Inconsistent input of files (%3d) and/or states (%3d).", nFiles, nStates));
       return this;
     }
 
     boolean autodetect = false;
     if (nStates > 2) {
       autodetect = true;
       lambdaValues = new double[nStates];
       for (int i = 0; i < nStates; i++) {
         lambdaValues[i] = alchemicalOptions.getInitialLambda(nStates, i, true);
       }
     } else {
       // Otherwise we assume two ensembles at the given lambda values.
       lambdaValues = new double[2];
       lambdaValues[0] = alchemicalOptions.getInitialLambda(2, 0, true);
       lambdaValues[1] = lambda2;
       nStates = 2;
     }
 
     // Could set "getInitialLambda"'s quiet flag to false, but better logging here?
     logger.info(" Lambda values for each window: ");
     int nLambda = lambdaValues.length;
     for (int i = 0; i < nLambda; i++) {
       logger.info(format(" Window %3d: %6.4f", i, lambdaValues[i]));
     }
 
     // Open assemblies if not using Tinker BAR files.
     boolean isPBC;
 
     // Allocate space for each topology
     int threadsPerTopology = topologyOptions.getThreadsPerTopology(numTopologies);
     topologies = new MolecularAssembly[numTopologies];
     SystemFilter[] openers = new SystemFilter[numTopologies];
 
     alchemicalOptions.setAlchemicalProperties();
     topologyOptions.setAlchemicalProperties(numTopologies);
 
     if (numTopologies == 2) {
       logger.info(format(" Initializing two topologies for each window."));
     } else {
       logger.info(format(" Initializing a single topology for each window."));
     }
 
     for (int i = 0; i < numTopologies; i++) {
       MolecularAssembly ma = alchemicalOptions.openFile(algorithmFunctions, topologyOptions,
           threadsPerTopology, filenames.get(i), i);
       topologies[i] = ma;
       openers[i] = algorithmFunctions.getFilter();
     }
 
     StringBuilder sb = new StringBuilder(format(
         "\n Using BAR to analyze a free energy change for %s\n ", filenames));
     potential = (CrystalPotential) topologyOptions.assemblePotential(topologies, sb);
     Crystal unitCell = potential.getCrystal().getUnitCell();
     isPBC = includeVolume && !unitCell.aperiodic();
 
     String[][] fullFilePaths;
     String directoryPath;
     if (nFiles > 0) {
       // For Dual-Topology systems that only compare two states, simplify filePaths to use only the 2 files belonging
       // to each ensemble
       int dtIndex = 0;
       if (numTopologies == 2 && nFiles == 4) {
         fullFilePaths = new String[nStates][2];
         dtIndex = 2;
       } else {
         fullFilePaths = new String[nStates][nFiles];
       }
 
       // Loop over ensembles
       for (int i = 0; i < nStates; i++) {
         // Loop over user supplied files.
         for (int j = 0; j < nFiles; j++) {
           // For Dual-Topology, start at index 2 for second ensemble
           if (i == 1 && j == 0) {
             j = dtIndex;
           }
           File file = new File(files[j]);
           directoryPath = file.getAbsoluteFile().getParent() + File.separator;
           String archiveName;
           if (sortedArc) {
             archiveName = FilenameUtils.getBaseName(files[j]) + "_E" + String.valueOf(i) + ".arc";
           } else {
             archiveName = FilenameUtils.getBaseName(files[j]) + ".arc";
           }
           if (!autodetect) {
             // Path to a file in the same directory as supplied archives.
             fullFilePaths[i][j - dtIndex] = directoryPath + File.separator + archiveName;
           } else {
             // Paths to auto-detected subdirectories.
             fullFilePaths[i][j - dtIndex] = directoryPath + i + File.separator + archiveName;
           }
           // For Dual-Topology, stop after two files for first ensemble
           if (i == 0 && j == 1) {
             j += dtIndex * nFiles;
           }
         }
       }
 
       // Initialize the ParallelEnergy class.
       ParallelStateEnergy pe = new ParallelStateEnergy(nStates, lambdaValues,
           topologies, potential, fullFilePaths, openers);
 
       // Evaluate energies from snapshots.
       double[][] energiesLow = new double[nStates][];
       double[][] energiesAt = new double[nStates][];
       double[][] energiesHigh = new double[nStates][];
       double[][] volume = new double[nStates][];
       pe.evaluateStates(energiesLow, energiesAt, energiesHigh, volume);
 
       // Only node 0 will write out Tinker BAR files.
       if (pe.getRank() != 0) {
         return this;
       }
 
       // Create file objects to write out TINKER style bar files.
       File file = new File(files[0]);
       directoryPath = file.getAbsoluteFile().getParent() + File.separator;
       String tinkerDirectoryPath = directoryPath + File.separator + "windows";
       File directory = new File(tinkerDirectoryPath);
       String barFilePath = tinkerDirectoryPath + File.separator;
       directory.mkdir();
 
       for (int state = 0; state < nStates - 1; state++) {
         File xyzFile = new File(filenames.get(0));
         BARFilter barFilter;
         barFilter = new BARFilter(xyzFile, energiesAt[state], energiesHigh[state], energiesLow[state + 1],
             energiesAt[state + 1], volume[state], volume[state + 1], temperature, temperature);
         String barFileName = barFilePath + "window_" + String.valueOf(state) + ".bar";
         // Write out the TINKER style bar file. An existing file will be overwritten.
         barFilter.writeFile(barFileName, isPBC, false);
       }
     }
 
     return this;
   }
 
   /**
    * Read energy and volume values from BAR files. The first dimension of the energy arrays
    * corresponds to the state index. The second dimension corresponds to the snapshot index.
    * <p>
    * The first dimension of each array should be allocated to the number of states prior
    * to calling this method.
    *
    * @param barFilters   The BAR filters to use.
    * @param energyLow    The energy of each snapshot in state L evaluated at L-dL.
    * @param energyAt     The energy of each snapshot in L evaluated at L.
    * @param energyHigh   The energy from state L evaluated at L+dL.
    * @param volume       The volume of each snapshot from state L.
    * @param temperatures The temperatures for each state.
    */
   void readBARFiles(BARFilter[] barFilters,
                     double[][] energyLow, double[][] energyAt,
                     double[][] energyHigh, double[][] volume,
                     double[] temperatures) {
 
     // Read energy values from BAR files.
     for (BARFilter barFilter : barFilters) {
       barFilter.readFile();
     }
 
     // Assign values to the state arrays.
     for (int state = 0; state < nStates; state++) {
       if (state == 0) {
         energyAt[state] = barFilters[state].getE1l1();
         energyHigh[state] = barFilters[state].getE1l2();
         volume[state] = barFilters[state].getVolume1();
         temperatures[state] = barFilters[state].getTemperature1();
       } else if (state == nStates - 1) {
         energyLow[state] = barFilters[state - 1].getE2l1();
         energyAt[state] = barFilters[state - 1].getE2l2();
         volume[state] = barFilters[state - 1].getVolume2();
         temperatures[state] = barFilters[state - 1].getTemperature2();
       } else {
         energyLow[state] = barFilters[state - 1].getE2l1();
         energyAt[state] = barFilters[state].getE1l1();
         energyHigh[state] = barFilters[state].getE1l2();
         volume[state] = barFilters[state].getVolume1();
         temperatures[state] = barFilters[state].getTemperature1();
       }
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (potential == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = new ArrayList<>();
       potentials.add(potential);
     }
     return potentials;
   }
 
   /**
    * Obtain the Free Energy Difference reporter for this class.
    *
    * @return The Free Energy Difference reporter.
    */
   public FreeEnergyDifferenceReporter getReporter() {
     return reporter;
   }
 
 }