// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2026.
   //
   // 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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  // exception statement from your version.
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  // ******************************************************************************
  package ffx.xray;
  
  import ffx.algorithms.misc.AlgorithmsTest;
  import ffx.crystal.HKL;
  import ffx.potential.bonded.Atom;
  import ffx.potential.parameters.AtomType;
  import ffx.xray.scatter.XRayFormFactor;
  import ffx.xray.scatter.XRayScatteringParameters;
  import org.junit.Before;
  import org.junit.Test;
  
  import static java.lang.String.format;
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertNotNull;
  
  /**
   * @author Timothy D. Fenn
   */
  public class FormFactorTest extends AlgorithmsTest {
  
    private XRayFormFactor carbonFormFactor;
  
    @Before
    public void setUp() {
      double[] d = new double[3];
      double[] anisou = new double[6];
      anisou[0] = anisou[1] = anisou[2] = 1.0;
      anisou[3] = anisou[4] = anisou[5] = 0.0;
      Atom carbon = new Atom(1, "C", 'A', d, "ALA", 1, 'A', 1.0, 20.0, "A");
      AtomType atomType = new AtomType(1, 1, "C", null, 6, 12.01, 1);
      carbon.setAtomType(atomType);
      carbon.setAltLoc('A');
      carbon.setAnisou(anisou);
      carbonFormFactor = new XRayFormFactor(carbon, false, 0.0);
    }
  
    @Test
    public void testCarbonFF() {
      assertNotNull(" Carbon form factors should exist", XRayScatteringParameters.getFormFactor(6,0, false));
      double[][] formFactor = XRayScatteringParameters.getFormFactor(6, 0, false).formFactor();
      assertEquals(" Carbon form factors", 5, (int) formFactor[0][0]);
      assertEquals(" Carbon form factors", 2.09921, formFactor[1][0], 0.0001);
      assertEquals(" Carbon form factors", 13.18997, formFactor[2][0], 0.0001);
    }
  
    @Test
    public void testCarbonfrho() {
      HKL hkl = new HKL(1, 1, 1);
      assertEquals("carbon (1 1 1) structure factor", 2.3986e-26,
          carbonFormFactor.f(hkl), 1e-30);
  
      double[] xyz = {1.0, 1.0, 1.0};
      assertEquals("carbon (1 1 1) electron density", 0.081937,
          carbonFormFactor.rho(0.0, 1.0, xyz), 0.000001);
    }
  
    @Test
    public void testFormFactors() {
      for (int i = 1; i <= 18; i++) {
        XRayScatteringParameters parameters = XRayScatteringParameters.getFormFactor(i, 0, false);
        double[][] formFactor = parameters.formFactor();
        double sum = 0.0;
       for (int j = 0; j < 6; j++) {
         sum += formFactor[1][j];
       }
       assertEquals(format(" Form factor 6G sum for %s", parameters), i, sum, 1e-2);
     }
   }
 
   @Test
   public void testFormFactors3G() {
     for (int i = 1; i <= 18; i++) {
       XRayScatteringParameters parameters = XRayScatteringParameters.getFormFactor(i, 0, true);
       double[][] formFactor = parameters.formFactor();
       double sum = 0.0;
       for (int j = 0; j < parameters.numberOfGaussians(); j++) {
         sum += formFactor[1][j];
       }
       assertEquals(format(" Form factor 3G sum for %s", parameters), i, sum, 1e-1);
     }
   }
 }