//******************************************************************************
   //
   // 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.
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  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
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  //******************************************************************************
  package ffx.algorithms.commands.test;
  
  import edu.rit.pj.Comm;
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.utilities.FFXCommand;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Unmatched;
  
  import java.util.ArrayList;
  import java.util.List;
  
  import static java.lang.String.format;
  
  /**
   * The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another
   * FFXScript multiple times across a pH range. It uses MPI for parallel execution.
   * <br>
   * Usage:
   * <br>
   * ffxc test.ManyBodyPhScan [options] &lt;script-name&gt; [script-args...]
   */
  @Command(description = " Run a pH Scan with ManyBody.", name = "test.ManyBodyPHScan")
  public class ManyBodyPhScan extends AlgorithmsCommand {
  
    /**
     * --spH --startpH Lower end of the pH range to be evaluated.
     */
    @Option(names = {"--spH", "--startpH"}, paramLabel = "0.0", defaultValue = "0.0",
        description = "Lower end of the pH range to be evaluated.")
    private double start;
  
    /**
     * --epH --endpH Upper end of the pH range to be evaluated.
     */
    @Option(names = {"--epH", "--endpH"}, paramLabel = "14.0", defaultValue = "14.0",
        description = "Upper end of the pH range to be evaluated.")
    private double end;
  
    /**
     * --ns --nSteps Number of steps for the given pH range.
     */
    @Option(names = {"--ns", "--nSteps"}, paramLabel = "2.0", defaultValue = "2.0",
        description = "Number of steps for a given pH range.")
    private double nSteps;
  
    /**
     * The final argument(s) should be one or more filenames.
     */
    @Unmatched
    private List<String> unmatched;
  
    /**
     * ManyBodyPhScan Constructor.
     */
    public ManyBodyPhScan() {
      super();
    }
  
    /**
     * ManyBodyPhScan Constructor.
    * @param binding The Binding to use.
    */
   public ManyBodyPhScan(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * ManyBodyPhScan constructor that sets the command line arguments.
    * @param args Command line arguments.
    */
   public ManyBodyPhScan(String[] args) {
     super(args);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public ManyBodyPhScan run() {
 
     if (!init()) {
       return this;
     }
 
     // Set a flag to avoid double use of MPI in downstream commands.
     System.setProperty("pj.use.mpi", "false");
 
     Class<? extends FFXCommand> script = FFXCommand.getCommand(unmatched.get(0));
     Comm world = Comm.world();
     int numProc = world.size();
     int rank = world.rank();
 
     if (numProc > 1) {
       logger.info(format(" Number of processes:  %d", numProc));
       logger.info(format(" Rank of this process: %d", rank));
     }
 
     // Remove ManyBodyPHScan command.
     unmatched.remove(0);
 
     double stepSize = (end - start) / (nSteps - 1);
 
     int pHIndex = unmatched.indexOf("0.0");
     for (int i = 0; i < nSteps; i++) {
       double pHValue = start + (stepSize * i);
       List<String> commandArgs = new ArrayList<>();
       for (String arg : unmatched) {
         unmatched.set(pHIndex, String.valueOf(pHValue));
         commandArgs.add(arg);
       }
 
       // Create a Binding for command line arguments.
       FFXBinding binding = new FFXBinding();
       binding.setVariable("args", commandArgs);
 
       try {
         FFXCommand command = script.getDeclaredConstructor().newInstance();
         command.setBinding(binding);
         command.run();
       } catch (Exception e) {
         logger.info(format(" Exception for pH value: %s", pHValue));
       }
     }
     // Clear the pj.use.mpi flag.
     System.clearProperty("pj.use.mpi");
 
     return this;
 
   }
 }