Examples of TorsionGradients

Examples of name.mjw.jamber.util.TorsionGradients

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    Torsion torsion = new Torsion();
       
    assertEquals(-115.17206338216852, torsion.getAngle(i,j,k,l), delta);
   
    TorsionGradients gradients;
   
    gradients = torsion.getGradients(i,j,k,l);
   
    LOG.debug(gradients.getI());
    LOG.debug(gradients.getJ());
    LOG.debug(gradients.getK());
    LOG.debug(gradients.getL());
   
    // Correct Gradients
    Vector3d a = new Vector3d(-0.427895,  -0.383993,   0.458374 );
    Vector3d b = new Vector3d( 0.305333,   0.615610,  -0.638652 );
    Vector3d c = new Vector3d( 0.801409,  -0.417391,   0.178151 );
    Vector3d d = new Vector3d(-0.678846,   0.185773,   0.002127 );
   
    assertEquals(a.x, gradients.getI().x, delta );
    assertEquals(a.y, gradients.getI().y, delta );
    assertEquals(a.z, gradients.getI().z, delta );
   
    assertEquals(b.x, gradients.getJ().x, delta );
    assertEquals(b.y, gradients.getJ().y, delta );
    assertEquals(b.z, gradients.getJ().z, delta );
   
    assertEquals(c.x, gradients.getK().x, delta );
    assertEquals(c.y, gradients.getK().y, delta );
    assertEquals(c.z, gradients.getK().z, delta );
   
    assertEquals(d.x, gradients.getL().x, delta );
    assertEquals(d.y, gradients.getL().y, delta );
    assertEquals(d.z, gradients.getL().z, delta );
   
  }
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Examples of name.mjw.jamber.util.TorsionGradients

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    Point3d l = new Point3d(59.367950, 66.384277, 15.233553);

     
    Torsion torsion = new Torsion();
   
    TorsionGradients gradients;
   
    gradients = torsion.getGradients(i,j,k,l);
   
    // Correct Gradients
    Vector3d a = new Vector3d( 0.062885,  -0.469977,  -0.510851 );
    Vector3d b = new Vector3d(-0.267922,   0.730722,   0.747527 );
    Vector3d c = new Vector3d( 0.799196,  -0.529675,  -0.375642 );
    Vector3d d = new Vector3d(-0.594160,   0.268930,   0.138966 );
   
    LOG.debug(gradients.getI());
    LOG.debug(gradients.getJ());
    LOG.debug(gradients.getK());
    LOG.debug(gradients.getL());
           
    assertEquals(a.x, gradients.getI().x, delta );
    assertEquals(a.y, gradients.getI().y, delta );
    assertEquals(a.z, gradients.getI().z, delta );
   
    assertEquals(b.x, gradients.getJ().x, delta );
    assertEquals(b.y, gradients.getJ().y, delta );
    assertEquals(b.z, gradients.getJ().z, delta );
   
    assertEquals(c.x, gradients.getK().x, delta );
    assertEquals(c.y, gradients.getK().y, delta );
    assertEquals(c.z, gradients.getK().z, delta );
   
    assertEquals(d.x, gradients.getL().x, delta );
    assertEquals(d.y, gradients.getL().y, delta );
    assertEquals(d.z, gradients.getL().z, delta );
   
  }
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Examples of name.mjw.jamber.util.TorsionGradients

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    double unitForce = getAnalyticalGradient() / temp3d.length();

    Torsion gt = new Torsion();

    TorsionGradients grad = gt.getGradients(i.getPosition(), j.getPosition(),
        k.getPosition(), l.getPosition());

    Vector3d tempI = grad.getI();
    tempI.scale(unitForce);

    Vector3d tempJ = grad.getJ();
    tempJ.scale(unitForce);

    Vector3d tempK = grad.getK();
    tempK.scale(unitForce);

    Vector3d tempL = grad.getL();
    tempL.scale(unitForce);

    i.subForce(tempI);
    j.subForce(tempJ);
    k.subForce(tempK);
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