// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // 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
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.xray.parsers;
  
  import ffx.crystal.Crystal;
  
  import static org.apache.commons.math3.util.FastMath.pow;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  import java.io.BufferedWriter;
  import java.io.FileWriter;
  import java.io.PrintWriter;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * The CNSMapWriter class writes an output map that covers the unit cell (not the asymmetric unit).
   * The map is set up for passage into FFTs (the x-axis has +2 offset).
   *
   * @author Timothy D. Fenn
   * @see CCP4MapWriter
   * @since 1.0
   */
  public class CNSMapWriter {
  
    private static final Logger logger = Logger.getLogger(CNSMapWriter.class.getName());
    private final String filename;
    private final Crystal crystal;
    private final int nx, ny, nz;
  
    /**
     * Constructor for CNSMapWriter.
     *
     * @param nx an int.
     * @param ny an int.
     * @param nz an int.
     * @param crystal a {@link ffx.crystal.Crystal} object.
     * @param filename a {@link java.lang.String} object.
     */
    public CNSMapWriter(int nx, int ny, int nz, Crystal crystal, String filename) {
      this.nx = nx;
      this.ny = ny;
      this.nz = nz;
      this.crystal = crystal;
      this.filename = filename;
    }
  
    /**
     * write
     *
     * @param data an array of double.
     */
    public void write(double[] data) {
      try {
        StringBuilder sb = new StringBuilder();
        sb.append(String.format("\nwriting CNS map file: \"%s\"\n", filename));
  
        PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(filename)));
        double mean = 0.0;
        double sd = 0.0;
        out.println();
        out.println("       1");
        out.println("map from ffx");
        out.printf("%8d%8d%8d%8d%8d%8d%8d%8d%8d\n", nx, 0, nx - 1, ny, 0, ny - 1, nz, 0, nz - 1);
       out.printf(
           "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n",
           crystal.a, crystal.b, crystal.c, crystal.alpha, crystal.beta, crystal.gamma);
       out.println("ZYX");
       int n = 0;
       for (int k = 0; k < nz; k++) {
         out.printf("%8d\n", k);
         for (int j = 0; j < ny; j++) {
           for (int i = 0; i < nx; i++) {
             int index = 2 * (i + nx * (j + ny * k));
             out.printf("%12.5E", data[index]);
             n++;
             mean += (data[index] - mean) / n;
             if ((n % 6) == 0) {
               out.println();
             }
           }
         }
       }
 
       n = 0;
       for (int k = 0; k < nz; k++) {
         for (int j = 0; j < ny; j++) {
           for (int i = 0; i < nx; i++) {
             int index = 2 * (i + nx * (j + ny * k));
             sd += pow(data[index] - mean, 2.0);
             n++;
           }
         }
       }
       sd = sqrt(sd / n);
 
       out.println("   -9999");
       out.printf("%12.4E%12.4E\n", mean, sd);
       sb.append(String.format("map mean: %g standard dev.: %g", mean, sd));
       out.close();
       if (logger.isLoggable(Level.INFO)) {
         logger.info(sb.toString());
       }
     } catch (Exception e) {
       String message = "Fatal exception evaluating structure factors.\n";
       logger.log(Level.SEVERE, message, e);
       System.exit(-1);
     }
   }
 }