// ******************************************************************************
   //
   // 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,
  // 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.algorithms.commands;
  
  import static org.junit.Assert.assertEquals;
  
  import ffx.algorithms.dynamics.MolecularDynamics;
  import ffx.algorithms.misc.AlgorithmsTest;
  import java.util.Arrays;
  import java.util.Collection;
  import org.junit.Test;
  import org.junit.runner.RunWith;
  import org.junit.runners.Parameterized;
  import org.junit.runners.Parameterized.Parameters;
  
  /** @author Hernan V Bernabe */
  @RunWith(Parameterized.class)
  public class DynamicsNVETest extends AlgorithmsTest {
  
    private String info;
    private String filename;
    private double startingTotalEnergy;
    private double endKineticEnergy;
    private double endPotentialEnergy;
    private double endTotalEnergy;
    private double tolerance = 0.1;
  
    public DynamicsNVETest(
        String info,
        String filename,
        double startingTotalEnergy,
        double endKineticEnergy,
        double endPotentialEnergy,
        double endTotalEnergy) {
      this.info = info;
      this.filename = filename;
      this.startingTotalEnergy = startingTotalEnergy;
      this.endKineticEnergy = endKineticEnergy;
      this.endPotentialEnergy = endPotentialEnergy;
      this.endTotalEnergy = endTotalEnergy;
    }
  
    @Parameters
    public static Collection<Object[]> data() {
      return Arrays.asList(
          new Object[][] {
              {
                  "Acetamide Peptide NVE", // info
                  "acetamide_NVE.xyz", // filename
                  -25.1958, // startingTotalEnergy
                  4.5625, // endKineticEnergy
                  -29.8043, // endPotentialEnergy
                  -25.2418 // endTotalEnergy
              }
          });
    }
  
    @Test
    public void testDynamicsHelp() {
      // Set-up the input arguments for the script.
      String[] args = {"-h"};
      binding.setVariable("args", args);
  
      // Construct and evaluate the script.
     Dynamics dynamics = new Dynamics(binding).run();
     algorithmsScript = dynamics;
   }
 
   @Test
   public void testDynamicsNVE() {
 
     // Set-up the input arguments for the script.
     String[] args = {
         "-n", "10",
         "-t", "298.15",
         "-i", "VelocityVerlet",
         "-b", "Adiabatic",
         "-r", "0.001",
         getResourcePath(filename)
     };
     binding.setVariable("args", args);
 
     // Construct and evaluate the script.
     Dynamics dynamics = new Dynamics(binding).run();
     algorithmsScript = dynamics;
 
     MolecularDynamics molDyn = dynamics.getMolecularDynamics();
 
     // Assert that energy is conserved at the end of the dynamics trajectory.
     assertEquals(
         info + " Final kinetic energy", endKineticEnergy, molDyn.getKineticEnergy(), tolerance);
     assertEquals(
         info + " Final potential energy", endPotentialEnergy, molDyn.getPotentialEnergy(),
         tolerance);
     assertEquals(
         info + " Final total energy", startingTotalEnergy, molDyn.getTotalEnergy(), tolerance);
   }
 }