//******************************************************************************
   //
   // 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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  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
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  // 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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  //******************************************************************************
  package ffx.xray.commands.test;
  
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.PotentialCommand;
  import ffx.utilities.FFXBinding;
  import ffx.xray.DiffractionData;
  import ffx.xray.refine.RefinedParameter;
  import ffx.xray.refine.RefinementMode;
  import ffx.xray.refine.RefinementModel;
  import ffx.xray.XRayEnergy;
  import ffx.xray.cli.XrayOptions;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.util.ArrayList;
  import java.util.List;
  
  import static ffx.utilities.StringUtils.parseAtomRanges;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * The Gradient script evaluates the consistency of the energy and gradient.
   * <br>
   * Usage:
   * <br>
   * ffxc test.Gradient [options] &lt;filename&gt;
   */
  @Command(description = " Test the potential energy gradient.", name = "test.Gradient")
  public class Gradient extends PotentialCommand {
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    XrayOptions xrayOptions;
  
    /**
     * -d or --dx Finite-difference step size.
     */
    @Option(names = {"-d", "--dx"}, defaultValue = "1.0e-5", paramLabel = "1.0e-5",
        description = "Finite-difference step size.")
    public double dx = 1.0e-5;
  
    /**
     * --tol or --tolerance Gradient error tolerance.
     */
    @Option(names = {"--tol", "--tolerance"}, defaultValue = "1.0e-3",
        paramLabel = "1.0e-3 kcal/mol/param", description = "Gradient error tolerance.")
    public double tolerance = 1.0e-3;
  
    /**
     * --params or --gradientAtoms Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].
     */
    @Option(names = {"--params", "--gradientParams"}, paramLabel = "ALL", defaultValue = "ALL",
        description = "Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].")
    public String gradientParams = "ALL";
 
 
   /**
    * One or more filenames.
    */
   @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Diffraction input files.")
   private List<String> filenames;
 
   private MolecularAssembly[] molecularAssemblies;
   private DiffractionData diffractionData;
   private XRayEnergy xrayEnergy;
   public int nFailures = 0;
 
   /**
    * Gradient constructor.
    */
   public Gradient() {
     super();
   }
 
   /**
    * Gradient constructor.
    *
    * @param binding The Binding to use.
    */
   public Gradient(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * Gradient constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public Gradient(String[] args) {
     super(args);
   }
 
   /**
    * Execute the script.
    */
   @Override
   public Gradient run() {
 
     if (!init()) {
       return this;
     }
 
     xrayOptions.init();
 
     String filename;
     if (filenames != null && !filenames.isEmpty()) {
       // Each alternate conformer is returned in a separate MolecularAssembly.
       molecularAssemblies = potentialFunctions.openAll(filenames.getFirst());
       activeAssembly = molecularAssemblies[0];
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       molecularAssemblies = new MolecularAssembly[]{activeAssembly};
     }
 
     // Update the active filename
     filename = activeAssembly.getFile().getAbsolutePath();
 
     // Set active atoms for each assembly.
     for (MolecularAssembly assembly : molecularAssemblies) {
       atomSelectionOptions.setActiveAtoms(assembly);
     }
 
     // Combine script flags (in parseResult) with properties.
     CompositeConfiguration properties = activeAssembly.getProperties();
     xrayOptions.setProperties(parseResult, properties);
 
     // Set up diffraction data (can be multiple files)
     diffractionData = xrayOptions.getDiffractionData(filenames, molecularAssemblies, properties);
     diffractionData.scaleBulkFit();
     diffractionData.printStats();
     xrayEnergy = new XRayEnergy(diffractionData);
 
     RefinementModel refinementModel = diffractionData.getRefinementModel();
     RefinementMode refinementMode = refinementModel.getRefinementMode();
 
     logger.info("\n Testing the gradient of " + filename);
     logger.info(refinementMode.toString());
     logger.info(refinementModel.toString());
 
     int n = refinementModel.getNumParameters();
     double[] x = new double[n];
     double[] g = new double[n];
     // Collect the analytic gradient.
     refinementModel.getParameters(x);
     xrayEnergy.energyAndGradient(x, g);
 
     List<RefinedParameter> refinedParameters = refinementModel.getRefinedParameters();
     int numParameters = refinedParameters.size();
 
     List<Integer> parametersToTest;
     if (gradientParams.equalsIgnoreCase("NONE")) {
       logger.info(" The gradient of no parameters will be evaluated.");
       return this;
     } else if (gradientParams.equalsIgnoreCase("ALL")) {
       logger.info(" Checking the gradient for all parameters.\n");
       parametersToTest = new ArrayList<>();
       for (int i = 0; i < numParameters; i++) {
         parametersToTest.add(i);
       }
     } else {
       parametersToTest = parseAtomRanges(" Parameters", gradientParams, numParameters);
       logger.info(" Checking the gradient for parameters in the range: " + gradientParams + "\n");
     }
 
     for (Integer parameter : parametersToTest) {
       RefinedParameter refinedParameter = refinedParameters.get(parameter);
       int index = refinedParameter.getIndex();
       int numParams = refinedParameter.getNumberOfParameters();
       double[] grad = new double[numParams];
       double error = 0.0;
       // Collect the gradient
       for (int i = 0; i < numParams; i++) {
         double orig = x[index + i];
         x[index + i] = orig + dx;
         double eplus = xrayEnergy.energy(x);
         x[index + i] = orig - dx;
         double eminus = xrayEnergy.energy(x);
         x[index + i] = orig;
         grad[i] = (eplus - eminus) / (2.0 * dx);
         double diff = grad[i] - g[index + i];
         error += diff * diff;
       }
       error = sqrt(error);
       if (numParams == 1) {
         logger.info(format("\n Refinement parameter %d with index %d", parameter + 1, index));
       } else {
         logger.info(format("\n Refinement parameter %d with indices %d - %s",
             parameter + 1, index, index + numParams - 1));
       }
       logger.info(format(" %s", refinedParameter));
       if (error > tolerance) {
         logger.info(format("  Failed: %10.6f", error));
       } else {
         logger.info(format("  Passed: %10.6f", error));
       }
       StringBuilder numeric = new StringBuilder("  Numeric:  ");
       StringBuilder analytic = new StringBuilder("  Analytic: ");
       for (int i = 0; i < numParams; i++) {
         numeric.append(format(" %10.6f", grad[i]));
         analytic.append(format(" %10.6f", g[index + i]));
       }
       logger.info(numeric.toString());
       logger.info(analytic.toString());
     }
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials = getPotentialsFromAssemblies(molecularAssemblies);
     if (xrayEnergy != null) {
       potentials.add(xrayEnergy);
     }
     return potentials;
   }
 
 }