// ******************************************************************************
   //
   // 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.potential.groovy;
  
  import static org.apache.commons.math3.util.FastMath.floor;
  import static org.apache.commons.math3.util.FastMath.random;
  import static org.junit.Assert.assertEquals;
  
  import ffx.potential.groovy.test.Gradient;
  import ffx.potential.utils.PotentialTest;
  import org.junit.Test;
  
  /** JUnit Tests for the Volume Script */
  public class VolumeTest extends PotentialTest {
  
    private final double tolerance = 0.001;
  
    /**
     * Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
     */
    @Test
    public void testConnollyMolecularButane() {
      // Configure input arguments for the Volume script.
      String filepath = getResourcePath("butane.xyz");
      String[] args = {"-c", "-p", "1.4", "-m", filepath};
      binding.setVariable("args", args);
      // Construct and evaluate the Volume script.
      Volume volume = new Volume(binding).run();
      potentialScript = volume;
      assertEquals(79.85081214917432, volume.totalVolume, tolerance);
      assertEquals(98.14422780202705, volume.totalSurfaceArea, tolerance);
    }
  
    /** Test Connolly SEV & SASA with a 1.4 A exclude radius. */
    @Test
    public void testConnollyMolecularCrambin() {
      // Configure input arguments for the Volume script.
      String filepath = getResourcePath("crambin.xyz");
      String[] args = {"-c", "-m", "-p", "1.4", filepath};
      binding.setVariable("args", args);
  
      // Construct and evaluate the Volume script.
      Volume volume = new Volume(binding).run();
      potentialScript = volume;
      assertEquals(5222.628196815338, volume.totalVolume, tolerance);
      assertEquals(2326.375086471378, volume.totalSurfaceArea, tolerance);
    }
  
    /**
     * Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
     */
    @Test
    public void testConnollyMolecularEthylbenzene() {
      // Configure input arguments for the Volume script.
      String filepath = getResourcePath("ethylbenzene.xyz");
      String[] args = {"-c", "-p", "1.4", "-m", filepath};
      binding.setVariable("args", args);
  
      // Construct and evaluate the Volume script.
      Volume volume = new Volume(binding).run();
      potentialScript = volume;
      assertEquals(126.96932864947797, volume.totalVolume, tolerance);
      assertEquals(137.7753894764906, volume.totalSurfaceArea, tolerance);
    }
 
   /**
    * Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
    */
   @Test
   public void testConnollyMolecularHydrogenButane() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("butane.xyz");
     String[] args = {"-c", "-p", "1.4", "-m", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(119.0512090546068, volume.totalVolume, tolerance);
     assertEquals(132.598010667639, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with a 1.4 A exclude radius and hydrogen atoms. */
   @Test
   public void testConnollyMolecularHydrogenCrambin() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"-c", "-m", "-p", "1.4", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(5890.028072142157, volume.totalVolume, tolerance);
     assertEquals(2456.835858765312, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly molecular surface area and volume with hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollyMolecularHydrogenEthylbenzene() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {"-c", "-p", "1.4", "-m", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(165.83018235892447, volume.totalVolume, tolerance);
     assertEquals(171.91980284282084, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA without hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVButane() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("butane.xyz");
     String[] args = {"-c", "-p", "1.4", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(302.0524178356785, volume.totalVolume, tolerance);
     assertEquals(227.49657650050898, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVCrambin() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"-c", "-p", "1.4", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(8956.620463626994, volume.totalVolume, tolerance);
     assertEquals(3015.7687533888334, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA without hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVEthylbenzene() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {"-c", "-p", "1.4", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(418.96380636214514, volume.totalVolume, tolerance);
     assertEquals(287.56961427851286, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVHydrogenButane() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("butane.xyz");
     String[] args = {"-c", "-p", "1.4", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(402.708673112844, volume.totalVolume, tolerance);
     assertEquals(280.836964340470, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with a 1.4 A exclude radius and hydrogen atoms. */
   @Test
   public void testConnollySEVHydrogenCrambin() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"-c", "-p", "1.4", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(9804.262055253388, volume.totalVolume, tolerance);
     assertEquals(3142.106787870207, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVHydrogenEthylbenzene() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {"-c", "-p", "1.4", "-y", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(518.612603965319, volume.totalVolume, tolerance);
     assertEquals(340.264998320387, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test Connolly SEV & SASA with hydrogen and a 1.4 A exclude radius. */
   @Test
   public void testConnollySEVHydrogenEthylbenzeneDerivatives() {
     // Configure input arguments for the Gradient script.
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {"--tol", "5.0e-2", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Gradient script
     Gradient gradient = new Gradient(binding).run();
     potentialScript = gradient;
     assertEquals("Ethylbenzene gradient failures: ", 0, gradient.nFailures);
   }
 
   /** Test Connolly vdW volume and surface area (probe radius = 0.0). */
   @Test
   public void testConnollyVDWCrambin() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"-c", "-p", "0.0", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(4418.303482563956, volume.totalVolume, tolerance);
     assertEquals(4168.547763834282, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test GaussVol without hydrogen and a 0.4 A radii offset. */
   @Test
   public void testGaussVolButane() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("butane.xyz");
     String[] args = {"-o", "0.4", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(125.5120767378517, volume.totalVolume, tolerance);
     assertEquals(134.50524040566165, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test GaussVol without hydrogen and a 0.0 A radii offset. */
   @Test
   public void testGaussVolCrambin() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"-o", "0.0", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(4371.667466648112, volume.totalVolume, tolerance);
     assertEquals(3971.0619085859435, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test GaussVol derivatives. */
   @Test
   public void testGaussVolCrambinDerivatives() {
     // Configure input arguments for the Gradient script.
     System.setProperty("gkterm", "true");
     System.setProperty("cavmodel", "gauss-disp");
     // Choose a random atom to test.
     int atomID = (int) floor(random() * 642) + 1;
     String filepath = getResourcePath("crambin.xyz");
     String[] args = {"--ga", Integer.toString(atomID), filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Gradient script
     Gradient gradient = new Gradient(binding).run();
     potentialScript = gradient;
     assertEquals("Crambin gradient failures: ", 0, gradient.nFailures);
   }
 
   /** Test GaussVol without hydrogen and a 0.4 A radii offset. */
   @Test
   public void testGaussVolEthylbenzene() {
     // Configure input arguments for the Volume script.
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {"-o", "0.4", filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Volume script.
     Volume volume = new Volume(binding).run();
     potentialScript = volume;
     assertEquals(194.44960348422916, volume.totalVolume, tolerance);
     assertEquals(193.55314214639066, volume.totalSurfaceArea, tolerance);
   }
 
   /** Test GaussVol derivatives. */
   @Test
   public void testGaussVolHydrogenEthylbenzeneDerivatives() {
     // Configure input arguments for the Gradient script.
     System.setProperty("gkterm", "true");
     System.setProperty("cavmodel", "gauss-disp");
     
     String filepath = getResourcePath("ethylbenzene.xyz");
     String[] args = {filepath};
     binding.setVariable("args", args);
 
     // Construct and evaluate the Gradient script
     Gradient gradient = new Gradient(binding).run();
     potentialScript = gradient;
     assertEquals("Ethylbenzene gradient failures: ", 0, gradient.nFailures);
   }
 }