// ******************************************************************************
   //
   // 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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  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
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  // Place, Suite 330, Boston, MA 02111-1307 USA
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  // combined work based on this library. Thus, the terms and conditions of the
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  package ffx.algorithms.groovy;
  
  import ffx.algorithms.misc.AlgorithmsTest;
  import org.junit.Test;
  
  import static org.junit.Assert.assertEquals;
  
  /**
   * Tests many body optimization and the many body groovy script under global, box and monte carlo
   * parameter conditions.
   *
   * @author Mallory R. Tollefson
   */
  public class ManyBodyTest extends AlgorithmsTest {
  
    /**
     * Tests ManyBody.groovy and RotamerOptimization.java by running a box optimization simulation on a
     * small pdb file.
     */
    @Test
    public void testManyBodyBoxOptimization() {
      // Set-up the input arguments for the script.
      String[] args = {
          "-a", "5",
          "-L", "2",
          "--bL", "10",
          "--bB", "2",
          "--tC", "2",
          "--pr", "2",
          getResourcePath("5awl.pdb")
      };
      binding.setVariable("args", args);
      binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
  
      // Evaluate the script.
      ManyBody manyBody = new ManyBody(binding).run();
      algorithmsScript = manyBody;
  
      double expectedTotalPotential = -230.1392872420811;
      double actualTotalPotential = manyBody.getPotential().getTotalEnergy();
      assertEquals(expectedTotalPotential, actualTotalPotential, 1E-7);
  
      double expectedApproximateEnergy = -225.97693128995238;
      double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
      assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-7);
    }
  
    /**
     * Tests the restart file functionality for box optimization. The test applies a 1.5 angstrom
     * 2-body and 3-body cutoff but the restart file was generated using 2-body and 3-body cutoffs of 2
     * angstroms.
     */
    @Test
    public void testManyBodyBoxRestart() {
      // Set-up the input arguments for the script.
      String[] args = {
          "-a", "5",
          "--bL", "10",
          "--tC", "1.5",
          "-T", "--thC",
          "1.5", "--eR",
          getResourcePath("5awl.box.restart"),
         getResourcePath("5awl.pdb")
     };
     binding.setVariable("args", args);
     binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding).run();
     algorithmsScript = manyBody;
 
     double expectedTotalPotential = -230.13928724208006; //-221.48751140045158
     double actualTotalPotential =
         manyBody.getPotential().getTotalEnergy();
     assertEquals(expectedTotalPotential, actualTotalPotential, 1E-7);
 
     double expectedApproximateEnergy = -230.88286802981403;
     double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
     assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-7);
   }
 
   @Test
   public void testManyBodyGlobal() {
     // Set-up the input arguments for the script.
     String[] args = {
         "-a", "2", "-L", "2", "--tC", "2", getResourcePath("5awl.pdb")
     };
     binding.setVariable("args", args);
     binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding).run();
     algorithmsScript = manyBody;
 
     // Evaluate the script.
     manyBody.run();
     double expectedTotalPotential = -230.1392865715949;
     double actualTotalPotential = manyBody.getPotential().getTotalEnergy();
     assertEquals(expectedTotalPotential, actualTotalPotential, 1E-5);
 
     double expectedApproximateEnergy = -216.57578192741352;
     double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
     assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-5);
 
     // Delete restart file.
     manyBody.getManyBodyOptions().getRestartFile().delete();
   }
 
   @Test
   public void testManyBodyHelp() {
     // Set-up the input arguments for the Biotype script.
     String[] args = {"-h"};
     binding.setVariable("args", args);
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding).run();
     algorithmsScript = manyBody;
   }
 
   /**
    * Tests ManyBody.groovy and RotamerOptimization.java by running a monte carlo optimization
    * simulation on a small pdb file. Elimination criteria are not used during this test. A Monte
    * Carlo search is done on the permutations.
    */
   @Test
   public void testManyBodyMonteCarlo() {
 
     // These properties will be cleared automatically after the test.
     System.setProperty("polarization", "direct");
     System.setProperty("manybody-testing", "true");
     System.setProperty("manybody-testing-mc", "true");
 
     // Set-up the input arguments for the script.
     String[] args = {
         "-a", "2",
         "-L", "2",
         "--tC", "2",
         "--pr", "2",
         "--mC", "100",
         getResourcePath("5awl.pdb")
     };
     binding.setVariable("args", args);
     binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding);
     algorithmsScript = manyBody;
     manyBody.run();
 
     double expectedTotalPotential = -204.72742343060315;
     double actualTotalPotential = manyBody.getPotential().getTotalEnergy();
     assertEquals(expectedTotalPotential, actualTotalPotential, 1E-5);
 
     double expectedApproximateEnergy = -195.16120410395288;
     double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
     assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-5);
 
     // Delete restart file.
     manyBody.getManyBodyOptions().getRestartFile().delete();
   }
 
   /**
    * Tests the restart file functionality. The test applies a 1.5 angstrom 2-body and 3-body cutoff
    * but the restart file was generated using 2-body and 3-body cutoffs of 2 angstroms.
    */
   @Test
   public void testManyBodyRestart() {
     // Set-up the input arguments for the script.
     String[] args = {"-a", "2", "-L", "2", "--tC", "1.5", "-T", "--thC", "1.5", "--eR",
         getResourcePath("5awl.test.restart"),
         getResourcePath("5awl.pdb")
     };
     binding.setVariable("args", args);
     binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding).run();
     algorithmsScript = manyBody;
 
     double expectedTotalPotential = -230.33490844427203;
     double actualTotalPotential = manyBody.getPotential().getTotalEnergy();
     assertEquals(expectedTotalPotential, actualTotalPotential, 1E-5);
 
     double expectedApproximateEnergy = -296.824576745933;
     double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
     assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-5);
   }
 
   @Test
   public void testManyBodyTitration() {
     // Set-up the input arguments for the script.
     String[] args = {"--tR", "--pH", "7.0", "--eR",
         getResourcePath("DEHK.rot.restart"),
         getResourcePath("DEHK.rot.pdb")
     };
     binding.setVariable("args", args);
     binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
 
     // Evaluate the script.
     ManyBody manyBody = new ManyBody(binding).run();
     algorithmsScript = manyBody;
 
     double expectedTotalPotential = -321.72679980;
     double actualTotalPotential = manyBody.getPotential().getTotalEnergy();
     assertEquals(expectedTotalPotential, actualTotalPotential, 1E-5);
 
     double expectedApproximateEnergy = -227.523807;
     double actualApproximateEnergy = manyBody.getManyBodyOptions().getApproximate();
     //TODO: Adjust delta back to norm and determine why getApproximate() is returning funky values
     assertEquals(expectedApproximateEnergy, actualApproximateEnergy, 1E-0);
   }
 
 }