// ******************************************************************************
   //
   // 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
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  // ******************************************************************************
  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;
  
  /**
   * Test NVT dynamics on a waterbox.
   *
   * @author Hernan V. Bernabe
   */
  @RunWith(Parameterized.class)
  public class DynamicsNVTTest extends AlgorithmsTest {
  
    private String info;
    private String filename;
    private double finalTemp;
    private double tempTolerance = 0.01;
    private double endTotalEnergy;
    private double energyTolerance = 0.01;
  
    public DynamicsNVTTest(String info, String filename, double finalTemp, double endTotalEnergy) {
      this.info = info;
      this.filename = filename;
      this.finalTemp = finalTemp;
      this.endTotalEnergy = endTotalEnergy;
    }
  
    @Parameters
    public static Collection<Object[]> data() {
      return Arrays.asList(
          new Object[][] {
              {
                  "Water Box NVT", // info
                  "waterbox_eq.xyz", // filename
                  296.18798, // Final temperature.
                  -24952.08001403058 // Final total energy
              }
          });
    }
  
    @Test
    public void testDynamicsNVT() {
  
      // Set-up the input arguments for the script.
      String[] args = {
          "-n", "10",
          "-t", "298.15",
          "-i", "VelocityVerlet",
          "-b", "Bussi",
          "-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 temperature is within tolerance at the end of the dynamics trajectory.
     assertEquals(info + " End temperature for NVT test", finalTemp, molDyn.getTemperature(),
         tempTolerance);
 
     // Assert that the end total energy is withing the tolerance at the end of the dynamics
     // trajectory.
     assertEquals(info + " End total energy for NVT test and set random seed",
         endTotalEnergy, molDyn.getTotalEnergy(), energyTolerance);
   }
 }