//******************************************************************************
   //
   // 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,
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  // library, you may extend this exception to your version of the library, but
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  //******************************************************************************
  package ffx.potential.commands;
  
  import ffx.crystal.Crystal;
  import ffx.crystal.LatticeSystem;
  import ffx.potential.bonded.Atom;
  import ffx.potential.cli.PotentialCommand;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.BufferedWriter;
  import java.io.File;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.HashMap;
  import java.util.Iterator;
  import java.util.Map;
  
  import static java.lang.String.format;
  import static org.apache.commons.io.FilenameUtils.getName;
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  import static org.apache.commons.math3.util.FastMath.cos;
  
  /**
   * Generate Quantum Espresso (QE) input from an XYZ file.
   * <p>
   * Usage:
   * ffxc XYZtoQE [options] &lt;filename&gt;
   */
  @Command(name = "XYZtoQE", description = "Generate QE input from a XYZ file.")
  public class ExportQE extends PotentialCommand {
  
    /**
     * Number of structural optimization steps performed in this run.
     */
    @Option(names = {"--ns", "--nstep"}, paramLabel = "500", defaultValue = "500",
        description = "Number of structural optimization steps performed in this run.")
    private int nStep;
  
    /**
     * Convergence threshold on total energy (a.u) for ionic minimization.
     */
    @Option(names = {"--ec", "--etot_conv_thr"}, paramLabel = "1.0e-6", defaultValue = "1.0e-6",
        description = "Convergence threshold on total energy (a.u) for ionic minimization.")
    private double etotConvThr;
  
    /**
     * Convergence threshold on forces (a.u) for ionic minimization.
     */
    @Option(names = {"--ef", "--forc_conv_thr"}, paramLabel = "1.0e-4", defaultValue = "1.0e-4",
        description = "Convergence threshold on forces (a.u) for ionic minimization.")
    private double forcConvThr;
  
    /**
     * Kinetic energy cutoff (Ry) for wavefunctions.
     */
    @Option(names = {"--ke", "--ecutwfc"}, paramLabel = "50.0", defaultValue = "50.0",
        description = "Kinetic energy cutoff (Ry) for wavefunctions.")
    private double ecutwfc;
  
    /**
    * Kinetic energy cutoff (Ry) for charge density and potential.
    */
   @Option(names = {"--rho", "--ecutrho"}, paramLabel = "500.0", defaultValue = "500.0",
       description = "Kinetic energy cutoff (Ry) for charge density and potential.")
   private double ecutrho;
 
   /**
    * Maximum number of iterations in a SCF step.
    */
   @Option(names = {"--em", "--electron_maxstep"}, paramLabel = "1500", defaultValue = "1500",
       description = "Maximum number of iterations in a scf step.")
   private int electronMaxstep;
 
   /**
    * Convergence threshold for self consistency.
    */
   @Option(names = {"--ct", "--conv_thr"}, paramLabel = "1.0e-8", defaultValue = "1.0e-8",
       description = "Convergence threshold for self consistency.")
   private double convThr;
 
   /**
    * Mixing factor for self-consistency.
    */
   @Option(names = {"--mb", "--mixing_beta"}, paramLabel = "0.5", defaultValue = "0.5",
       description = "Mixing factor for self-consistency.")
   private double mixingBeta;
 
   /**
    * Perform QE calculation on hexagonal rather than rhombohedral representation.
    */
   @Option(names = {"--hx", "--hexagonal"}, paramLabel = "true", defaultValue = "true",
       description = "Perform QE on hexagonal system.")
   private boolean hexagonal;
 
   /**
    * The final argument should be one filename (XYZ).
    */
   @Parameters(arity = "1", paramLabel = "file",
       description = "XYZ file to be converted.")
   private String filename = null;
 
   public ExportQE() {
     super();
   }
 
   public ExportQE(FFXBinding binding) {
     super(binding);
   }
 
   public ExportQE(String[] args) {
     super(args);
   }
 
   @Override
   public ExportQE run() {
     // Init the context and bind variables.
     if (!init()) {
       return this;
     }
 
     // Load the MolecularAssembly.
     activeAssembly = getActiveAssembly(filename);
     if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     // Set the filename.
     filename = activeAssembly.getFile().getAbsolutePath();
     logger.info(format("\n Converting %s to QE format\n", filename));
 
     String dirString = getBaseDirString(filename);
     String name = removeExtension(getName(filename));
     File modelFile = new File(dirString + name + ".in");
 
     Crystal crystal = activeAssembly.getCrystal().getUnitCell();
     double xtalA = crystal.a;
     double xtalB = crystal.b;
     double xtalC = crystal.c;
 
     HashMap<String, Double> atomTypes = new HashMap<>();
     StringBuilder atomicPositions = new StringBuilder();
 
     Atom[] atoms = activeAssembly.getAtomArray();
     for (Atom atom : atoms) {
       if (!atomTypes.containsKey(atom.getName())) {
         atomTypes.put(atom.getName(), atom.getAtomType().atomicWeight);
       }
       double[] xyz = atom.getXYZ(null);
       crystal.toFractionalCoordinates(xyz, xyz);
       atomicPositions.append(format("%2s %16.12f %16.12f %16.12f%n", atom.getName(), xyz[0], xyz[1], xyz[2]));
     }
 
     try (BufferedWriter bwQE = new BufferedWriter(new FileWriter(modelFile))) {
       // general variables controlling the run
       bwQE.write(format("&CONTROL%n" +
           "\tcalculation = 'vc-relax',%n" +
           "\trestart_mode = 'from_scratch',%n" +
           "\tprefix = '%s',%n" +
           "\tetot_conv_thr = %6.4E,%n" +
           "\tforc_conv_thr = %6.4E,%n" +
           "\tnstep = %d,%n" +
           "/%n", name, etotConvThr, forcConvThr, nStep));
 
       // structural information on the system under investigation
       bwQE.write(format("&SYSTEM%n" +
               "\tspace_group = %d,%n" +
               "\tnat = %d,%n" +
               "\tntyp = %d,%n" +
               "\ta = %16.12f%n" +
               "\tb = %16.12f%n" +
               "\tc = %16.12f%n" +
               "\tcosAB = %16.12f%n" +
               "\tcosAC = %16.12f%n" +
               "\tcosBC = %16.12f%n" +
               "\tecutwfc = %6.4f,%n" +
               "\tecutrho = %6.4f,%n" +
               "\tvdw_corr = 'XDM',%n",
           crystal.spaceGroup.number,
           activeAssembly.getAtomList().size(),
           atomTypes.size(),
           xtalA, xtalB, xtalC,
           cos(crystal.gamma), cos(crystal.beta), cos(crystal.alpha),
           ecutwfc, ecutrho));
       if (crystal.spaceGroup.latticeSystem == LatticeSystem.HEXAGONAL_LATTICE) {
         bwQE.write("\trhombohedral = .FALSE.,\n");
       }
       bwQE.write("/\n");
 
       // electronic variables: self-consistency, smearing
       bwQE.write(format("&ELECTRONS%n" +
           "\telectron_maxstep = %d,%n" +
           "\tconv_thr = %6.4E,%n" +
           "\tscf_must_converge = .TRUE.,%n" +
           "\tmixing_beta = %5.3f,%n" +
           "/%n", electronMaxstep, convThr, mixingBeta));
 
       // ionic variables: relaxation, dynamics
       bwQE.write("&IONS\n" +
           "\tion_dynamics = 'bfgs',\n" +
           "/\n");
 
       // variable-cell optimization or dynamics
       bwQE.write("&CELL\n" +
           "\tcell_dynamics = 'bfgs',\n" +
           "/\n");
 
       // ATOMIC_SPECIES
       StringBuilder line = new StringBuilder();
       Iterator<Map.Entry<String, Double>> it = atomTypes.entrySet().iterator();
       while (it.hasNext()) {
         Map.Entry<String, Double> pair = it.next();
         line.append(" ").append(pair.getKey()).append(" ").append(pair.getValue())
             .append(" ").append(pair.getKey()).append(".b86bpbe.UPF\n");
       }
       bwQE.write("ATOMIC_SPECIES\n" + line + "\n");
 
       // ATOMIC_POSITIONS
       bwQE.write("ATOMIC_POSITIONS crystal_sg\n" + atomicPositions + "\n");
 
       // K_POINTS automatic
       int k1;
       int k2;
       int k3;
       if (xtalA < 5) {
         k1 = 8;
       } else if (xtalA <= 7) {
         k1 = 6;
       } else if (xtalA <= 12) {
         k1 = 4;
       } else {
         k1 = 2;
       }
       if (xtalB < 5) {
         k2 = 8;
       } else if (xtalB <= 7) {
         k2 = 6;
       } else if (xtalB <= 12) {
         k2 = 4;
       } else {
         k2 = 2;
       }
       if (xtalC < 5) {
         k3 = 8;
       } else if (xtalC <= 7) {
         k3 = 6;
       } else if (xtalC <= 12) {
         k3 = 4;
       } else {
         k3 = 2;
       }
       bwQE.write("K_POINTS automatic\n" + k1 + " " + k2 + " " + k3 + " 1 1 1\n");
     } catch (IOException e) {
       logger.severe(" Error writing QE input file: " + e.getMessage());
     }
 
     logger.info(format(" Saved QE file: %s", modelFile));
     return this;
   }
 }