src/primitives/Torsion.cpp

#include "primitives/Torsion.hpp"

namespace oopse {

Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt)
            : atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) {

}

void Torsion::calcForce() {

    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = atom2_->getPos();
    Vector3d pos3 = atom3_->getPos();
    Vector3d pos4 = atom4_->getPos();

    Vector3d r12 = pos1 - pos2;
    Vector3d r23 = pos2 - pos3;
    Vector3d r34 = pos3 - pos4;

    //  Calculate the cross products and distances
    Vector3d A = cross(r12,r23);
    double rA = A.length();
    Vector3d B = cross(r23,r34);
    double rB = B.length();
    Vector3d C = cross(r23,A);
    double rC = C.length();

    //  Calculate the sin and cos
    double cos_phi = (A*B)/(rA*rB);
    double sin_phi = (C*B)/(rC*rB);

    double phi= -atan2(sin_phi,cos_phi);

    double firstDerivative;
    torsionType_->calcForce(phi, firstDerivative, potential_);


    Vector3d f1,f2,f3;
    
    //  Normalize B
    rB = 1.0/rB;
    B *= rB;

    //  Next, we want to calculate the forces.  In order
    //  to do that, we first need to figure out whether the
    //  sin or cos form will be more stable.  For this,
    //  just look at the value of phi
    if (fabs(sin_phi) > 0.1) {
        //  use the sin version to avoid 1/cos terms

        rA = 1.0/rA;
        A *= rA;
        Vector3d dcosdA = rA*(cos_phi*A-B);
        Vector3d dcosdB = rB*(cos_phi*B-A);

        K1 = K1/sin_phi;

        //simple form
        //f1 = K1 * cross(r23, dcosdA);
        //f3 = K1 * cross(r23, dcosdB);
        //f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA));

        f1.x = K1*(r23.y*dcosdA.z - r23.z*dcosdA.y);
        f1.y = K1*(r23.z*dcosdA.x - r23.x*dcosdA.z);
        f1.z = K1*(r23.x*dcosdA.y - r23.y*dcosdA.x);

        f3.x = K1*(r23.z*dcosdB.y - r23.y*dcosdB.z);
        f3.y = K1*(r23.x*dcosdB.z - r23.z*dcosdB.x);
        f3.z = K1*(r23.y*dcosdB.x - r23.x*dcosdB.y);

        f2.x = K1*(r12.z*dcosdA.y - r12.y*dcosdA.z + r34.y*dcosdB.z - r34.z*dcosdB.y);
        f2.y = K1*(r12.x*dcosdA.z - r12.z*dcosdA.x + r34.z*dcosdB.x - r34.x*dcosdB.z);
        f2.z = K1*(r12.y*dcosdA.x - r12.x*dcosdA.y + r34.x*dcosdB.y - r34.y*dcosdB.x);
    } else {
        //  This angle is closer to 0 or 180 than it is to
        //  90, so use the cos version to avoid 1/sin terms

        //  Normalize C
        rC = 1.0/rC;
        C *= rC;
        Vector3d dsindC = rC*(sin_phi*C-B);
        Vector3d dsindB = rB*(sin_phi*B-C);

        K1 = -K1/cos_phi;

        f1.x = K1*((r23.y*r23.y + r23.z*r23.z)*dsindC.x - r23.x*r23.y*dsindC.y - r23.x*r23.z*dsindC.z);
        f1.y = K1*((r23.z*r23.z + r23.x*r23.x)*dsindC.y - r23.y*r23.z*dsindC.z - r23.y*r23.x*dsindC.x);
        f1.z = K1*((r23.x*r23.x + r23.y*r23.y)*dsindC.z - r23.z*r23.x*dsindC.x - r23.z*r23.y*dsindC.y);

        f3 = K1 *cross(dsindB,r23);

        f2.x = K1*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x + (2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y
                 + (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z);
        f2.y = K1*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y + (2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z
                 + (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x);
        f2.z = K1*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z + (2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x
                  +(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y);
    }

    atom1_->addFrc(f1);
    atom2_->addFrc(f2 - f1);
    atom3_->addFrc(f3 - f2);
    atom4_->addFrc(-f3);
    
}


      double K=0;       // energy
      double K1=0;      // force

  // get the dihedral information
  int multiplicity = value->multiplicity;

  //  Loop through the multiple parameter sets for this
  //  bond.  We will only loop more than once if this
  //  has multiple parameter sets from Charmm22
  for (int mult_num=0; mult_num<multiplicity; mult_num++)
  {
    /* get angle information */
    double k = value->values[mult_num].k * scale;
    double delta = value->values[mult_num].delta;
    int n = value->values[mult_num].n;

    //  Calculate the energy
    if (n)
    {
      //  Periodicity is greater than 0, so use cos form
      K += k*(1+cos(n*phi + delta));
      K1 += -n*k*sin(n*phi + delta);
    }
    else
    {
      //  Periodicity is 0, so just use the harmonic form
      double diff = phi-delta;
      if (diff < -PI)           diff += TWOPI;
      else if (diff > PI)       diff -= TWOPI;

      K += k*diff*diff;
      K1 += 2.0*k*diff;
    }
  } /* for multiplicity */


void Torsion::calc_forces(){
  
  /**********************************************************************
   * 
   * initialize vectors
   *
   ***********************************************************************/
  
  vect r_ab; /* the vector whose origin is a and end is b */
  vect r_cb; /* the vector whose origin is c and end is b */
  vect r_cd; /* the vector whose origin is c and end is b */
  vect r_cr1; /* the cross product of r_ab and r_cb */
  vect r_cr2; /* the cross product of r_cb and r_cd */

  double r_cr1_x2; /* the components of r_cr1 squared */
  double r_cr1_y2;
  double r_cr1_z2;
  
  double r_cr2_x2; /* the components of r_cr2 squared */
  double r_cr2_y2;
  double r_cr2_z2;

  double r_cr1_sqr; /* the length of r_cr1 squared */
  double r_cr2_sqr; /* the length of r_cr2 squared */
  
  double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */
  
  Vector3d aR, bR, cR, dR;
  Vector3d  aF, bF, cF, dF;

  aR = c_p_a->getPos();
  bR = c_p_b->getPos();
  cR = c_p_c->getPos();
  dR = c_p_d->getPos();

  r_ab.x = bR[0] - aR[0];
  r_ab.y = bR[1] - aR[1];
  r_ab.z = bR[2] - aR[2];
  r_ab.length  = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z));

  r_cb.x = bR[0] - cR[0];
  r_cb.y = bR[1] - cR[1];
  r_cb.z = bR[2] - cR[2];
  r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z));

  r_cd.x = dR[0] - cR[0];
  r_cd.y = dR[1] - cR[1];
  r_cd.z = dR[2] - cR[2];
  r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z));

  r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z;
  r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x;
  r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y;
  r_cr1_x2 = r_cr1.x * r_cr1.x;
  r_cr1_y2 = r_cr1.y * r_cr1.y;
  r_cr1_z2 = r_cr1.z * r_cr1.z;
  r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2;
  r_cr1.length = sqrt(r_cr1_sqr);

  r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z;
  r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x;
  r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y;
  r_cr2_x2 = r_cr2.x * r_cr2.x;
  r_cr2_y2 = r_cr2.y * r_cr2.y;
  r_cr2_z2 = r_cr2.z * r_cr2.z;
  r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2;
  r_cr2.length = sqrt(r_cr2_sqr);

  r_cr1_r_cr2 = r_cr1.length * r_cr2.length;

    //Vector3d pos1 = atom1_->getPos();
    //Vector3d pos2 = atom2_->getPos();
    //Vector3d pos3 = atom3_->getPos();
    //Vector3d pos4 = atom4_->getPos();
   
    //Vector3d r12 = pos2 - pos1;
    //Vector3d r32 = pos2 - pos3;
    //Vector3d r34 = pos4 - pos3;

    //A = cross(r12, r32);
    //B = cross(r32, r34);
    
    //rA = A.length();  
    //rB = B.length();
  
  /**********************************************************************
   *
   * dot product and angle calculations 
   *
   ***********************************************************************/
  
  double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */
  double cos_phi; /* the cosine of the torsion angle */

  cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z;
  
  cos_phi = cr1_dot_cr2 / r_cr1_r_cr2;
  
   /* adjust for the granularity of the numbers for angles near 0 or pi */

  if(cos_phi > 1.0) cos_phi = 1.0;
  if(cos_phi < -1.0) cos_phi = -1.0;

    //cos_phi = dot (A, B) / (rA * rB);
    //if (cos_phi > 1.0) {
    //  cos_phi = 1.0;
    //}
    //if (cos_phi < -1.0) {
    //  cos_phi = -1.0;
    //}


  /********************************************************************
   *
   * This next section calculates derivatives needed for the force
   * calculation
   *
   ********************************************************************/


  /* the derivatives of cos phi with respect to the x, y,
     and z components of vectors cr1 and cr2. */
  double d_cos_dx_cr1;
  double d_cos_dy_cr1;
  double d_cos_dz_cr1;
  double d_cos_dx_cr2;
  double d_cos_dy_cr2;
  double d_cos_dz_cr2;

  d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr;
  d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr;
  d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr;

  d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr;
  d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr;
  d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr;

  //Vector3d dcosdA = B /(rA * rB) - cos_phi  /(rA * rA) * A;
  //Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize());
  //Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize());

  /***********************************************************************
   *
   * Calculate the actual forces and place them in the atoms. 
   *
   ***********************************************************************/

  double force; /*the force scaling factor */

  force = torsion_force(cos_phi);

  aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y);
  aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z);
  aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x);

  bF[0] = force * (  d_cos_dy_cr1 * (r_ab.z - r_cb.z)
           - d_cos_dy_cr2 *  r_cd.z   
           + d_cos_dz_cr1 * (r_cb.y - r_ab.y)
           + d_cos_dz_cr2 *  r_cd.y);
  bF[1] = force * (  d_cos_dx_cr1 * (r_cb.z - r_ab.z)
           + d_cos_dx_cr2 *  r_cd.z   
           + d_cos_dz_cr1 * (r_ab.x - r_cb.x)
           - d_cos_dz_cr2 *  r_cd.x);
  bF[2] = force * (  d_cos_dx_cr1 * (r_ab.y - r_cb.y)
           - d_cos_dx_cr2 *  r_cd.y   
           + d_cos_dy_cr1 * (r_cb.x - r_ab.x)
           + d_cos_dy_cr2 *  r_cd.x);

  cF[0] = force * (- d_cos_dy_cr1 *  r_ab.z
           - d_cos_dy_cr2 * (r_cb.z - r_cd.z)
           + d_cos_dz_cr1 *  r_ab.y
           - d_cos_dz_cr2 * (r_cd.y - r_cb.y));
  cF[1] = force * (  d_cos_dx_cr1 *  r_ab.z
           - d_cos_dx_cr2 * (r_cd.z - r_cb.z)
           - d_cos_dz_cr1 *  r_ab.x
           - d_cos_dz_cr2 * (r_cb.x - r_cd.x));
  cF[2] = force * (- d_cos_dx_cr1 *  r_ab.y
           - d_cos_dx_cr2 * (r_cb.y - r_cd.y)
           + d_cos_dy_cr1 *  r_ab.x
           - d_cos_dy_cr2 * (r_cd.x - r_cb.x));

  dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y);
  dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z);
  dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x);


  c_p_a->addFrc(aF);
  c_p_b->addFrc(bF);
  c_p_c->addFrc(cF);
  c_p_d->addFrc(dF);

    //double firstDerivative;
    //bondType_->calcForce(cos_phi, firstDerivative, potential_);
    //f1 = force * cross (dcosdA, r32);
    //f2 =
    //f3 = 
    //f4 = force * cross(dcosdB, r32);
    //atom1_->addFrc(f1);
    //atom2_->addFrc(f2);
    //atom3_->addFrc(f3);
    //atom4_->addFrc(f4);

  
}

}
Revision:	1742
Committed:	Tue Nov 16 20:36:18 2004 UTC (19 years, 9 months ago) by tim
File size:	11614 byte(s)
Log Message:	BondType, BendType and TorsionType
#	User	Rev	Content
1	tim	1742	#include "primitives/Torsion.hpp"
2	tim	1692
3	tim	1742	namespace oopse {
4
5			Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt)
6			: atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) {
7
8	tim	1692	}
9
10	tim	1742	void Torsion::calcForce() {
11	tim	1692
12	tim	1742	Vector3d pos1 = atom1_->getPos();
13			Vector3d pos2 = atom2_->getPos();
14			Vector3d pos3 = atom3_->getPos();
15			Vector3d pos4 = atom4_->getPos();
16
17			Vector3d r12 = pos1 - pos2;
18			Vector3d r23 = pos2 - pos3;
19			Vector3d r34 = pos3 - pos4;
20
21			// Calculate the cross products and distances
22			Vector3d A = cross(r12,r23);
23			double rA = A.length();
24			Vector3d B = cross(r23,r34);
25			double rB = B.length();
26			Vector3d C = cross(r23,A);
27			double rC = C.length();
28
29			// Calculate the sin and cos
30			double cos_phi = (AB)/(rArB);
31			double sin_phi = (CB)/(rCrB);
32
33			double phi= -atan2(sin_phi,cos_phi);
34
35			double firstDerivative;
36			torsionType_->calcForce(phi, firstDerivative, potential_);
37
38
39			Vector3d f1,f2,f3;
40
41			// Normalize B
42			rB = 1.0/rB;
43			B *= rB;
44
45			// Next, we want to calculate the forces. In order
46			// to do that, we first need to figure out whether the
47			// sin or cos form will be more stable. For this,
48			// just look at the value of phi
49			if (fabs(sin_phi) > 0.1) {
50			// use the sin version to avoid 1/cos terms
51
52			rA = 1.0/rA;
53			A *= rA;
54			Vector3d dcosdA = rA(cos_phiA-B);
55			Vector3d dcosdB = rB(cos_phiB-A);
56
57			K1 = K1/sin_phi;
58
59			//simple form
60			//f1 = K1 * cross(r23, dcosdA);
61			//f3 = K1 * cross(r23, dcosdB);
62			//f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA));
63
64			f1.x = K1(r23.ydcosdA.z - r23.z*dcosdA.y);
65			f1.y = K1(r23.zdcosdA.x - r23.x*dcosdA.z);
66			f1.z = K1(r23.xdcosdA.y - r23.y*dcosdA.x);
67
68			f3.x = K1(r23.zdcosdB.y - r23.y*dcosdB.z);
69			f3.y = K1(r23.xdcosdB.z - r23.z*dcosdB.x);
70			f3.z = K1(r23.ydcosdB.x - r23.x*dcosdB.y);
71
72			f2.x = K1(r12.zdcosdA.y - r12.ydcosdA.z + r34.ydcosdB.z - r34.z*dcosdB.y);
73			f2.y = K1(r12.xdcosdA.z - r12.zdcosdA.x + r34.zdcosdB.x - r34.x*dcosdB.z);
74			f2.z = K1(r12.ydcosdA.x - r12.xdcosdA.y + r34.xdcosdB.y - r34.y*dcosdB.x);
75			} else {
76			// This angle is closer to 0 or 180 than it is to
77			// 90, so use the cos version to avoid 1/sin terms
78
79			// Normalize C
80			rC = 1.0/rC;
81			C *= rC;
82			Vector3d dsindC = rC(sin_phiC-B);
83			Vector3d dsindB = rB(sin_phiB-C);
84
85			K1 = -K1/cos_phi;
86
87			f1.x = K1((r23.yr23.y + r23.zr23.z)dsindC.x - r23.xr23.ydsindC.y - r23.xr23.zdsindC.z);
88			f1.y = K1((r23.zr23.z + r23.xr23.x)dsindC.y - r23.yr23.zdsindC.z - r23.yr23.xdsindC.x);
89			f1.z = K1((r23.xr23.x + r23.yr23.y)dsindC.z - r23.zr23.xdsindC.x - r23.zr23.ydsindC.y);
90
91			f3 = K1 *cross(dsindB,r23);
92
93			f2.x = K1(-(r23.yr12.y + r23.zr12.z)dsindC.x + (2.0r23.xr12.y - r12.xr23.y)dsindC.y
94			+ (2.0r23.xr12.z - r12.xr23.z)dsindC.z + dsindB.zr34.y - dsindB.yr34.z);
95			f2.y = K1(-(r23.zr12.z + r23.xr12.x)dsindC.y + (2.0r23.yr12.z - r12.yr23.z)dsindC.z
96			+ (2.0r23.yr12.x - r12.yr23.x)dsindC.x + dsindB.xr34.z - dsindB.zr34.x);
97			f2.z = K1(-(r23.xr12.x + r23.yr12.y)dsindC.z + (2.0r23.zr12.x - r12.zr23.x)dsindC.x
98			+(2.0r23.zr12.y - r12.zr23.y)dsindC.y + dsindB.yr34.x - dsindB.xr34.y);
99			}
100
101			atom1_->addFrc(f1);
102			atom2_->addFrc(f2 - f1);
103			atom3_->addFrc(f3 - f2);
104			atom4_->addFrc(-f3);
105
106			}
107
108
109			double K=0; // energy
110			double K1=0; // force
111
112			// get the dihedral information
113			int multiplicity = value->multiplicity;
114
115			// Loop through the multiple parameter sets for this
116			// bond. We will only loop more than once if this
117			// has multiple parameter sets from Charmm22
118			for (int mult_num=0; mult_num<multiplicity; mult_num++)
119			{
120			/* get angle information */
121			double k = value->values[mult_num].k * scale;
122			double delta = value->values[mult_num].delta;
123			int n = value->values[mult_num].n;
124
125			// Calculate the energy
126			if (n)
127			{
128			// Periodicity is greater than 0, so use cos form
129			K += k(1+cos(nphi + delta));
130			K1 += -nksin(n*phi + delta);
131			}
132			else
133			{
134			// Periodicity is 0, so just use the harmonic form
135			double diff = phi-delta;
136			if (diff < -PI) diff += TWOPI;
137			else if (diff > PI) diff -= TWOPI;
138
139			K += kdiffdiff;
140			K1 += 2.0kdiff;
141			}
142			} /* for multiplicity */
143
144
145	tim	1692	void Torsion::calc_forces(){
146
147			/**********************************************************************
148			*
149			* initialize vectors
150			*
151			***********************************************************************/
152
153			vect r_ab; /* the vector whose origin is a and end is b */
154			vect r_cb; /* the vector whose origin is c and end is b */
155			vect r_cd; /* the vector whose origin is c and end is b */
156			vect r_cr1; /* the cross product of r_ab and r_cb */
157			vect r_cr2; /* the cross product of r_cb and r_cd */
158
159			double r_cr1_x2; /* the components of r_cr1 squared */
160			double r_cr1_y2;
161			double r_cr1_z2;
162
163			double r_cr2_x2; /* the components of r_cr2 squared */
164			double r_cr2_y2;
165			double r_cr2_z2;
166
167			double r_cr1_sqr; /* the length of r_cr1 squared */
168			double r_cr2_sqr; /* the length of r_cr2 squared */
169
170			double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */
171
172	tim	1701	Vector3d aR, bR, cR, dR;
173	tim	1742	Vector3d aF, bF, cF, dF;
174	tim	1692
175			aR = c_p_a->getPos();
176			bR = c_p_b->getPos();
177			cR = c_p_c->getPos();
178			dR = c_p_d->getPos();
179
180			r_ab.x = bR[0] - aR[0];
181			r_ab.y = bR[1] - aR[1];
182			r_ab.z = bR[2] - aR[2];
183			r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z));
184
185			r_cb.x = bR[0] - cR[0];
186			r_cb.y = bR[1] - cR[1];
187			r_cb.z = bR[2] - cR[2];
188			r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z));
189
190			r_cd.x = dR[0] - cR[0];
191			r_cd.y = dR[1] - cR[1];
192			r_cd.z = dR[2] - cR[2];
193			r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z));
194
195			r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z;
196			r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x;
197			r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y;
198			r_cr1_x2 = r_cr1.x * r_cr1.x;
199			r_cr1_y2 = r_cr1.y * r_cr1.y;
200			r_cr1_z2 = r_cr1.z * r_cr1.z;
201			r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2;
202			r_cr1.length = sqrt(r_cr1_sqr);
203
204			r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z;
205			r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x;
206			r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y;
207			r_cr2_x2 = r_cr2.x * r_cr2.x;
208			r_cr2_y2 = r_cr2.y * r_cr2.y;
209			r_cr2_z2 = r_cr2.z * r_cr2.z;
210			r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2;
211			r_cr2.length = sqrt(r_cr2_sqr);
212
213			r_cr1_r_cr2 = r_cr1.length * r_cr2.length;
214
215	tim	1742	//Vector3d pos1 = atom1_->getPos();
216			//Vector3d pos2 = atom2_->getPos();
217			//Vector3d pos3 = atom3_->getPos();
218			//Vector3d pos4 = atom4_->getPos();
219
220			//Vector3d r12 = pos2 - pos1;
221			//Vector3d r32 = pos2 - pos3;
222			//Vector3d r34 = pos4 - pos3;
223
224			//A = cross(r12, r32);
225			//B = cross(r32, r34);
226
227			//rA = A.length();
228			//rB = B.length();
229
230	tim	1692	/**********************************************************************
231			*
232			* dot product and angle calculations
233			*
234			***********************************************************************/
235
236			double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */
237			double cos_phi; /* the cosine of the torsion angle */
238
239			cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z;
240
241			cos_phi = cr1_dot_cr2 / r_cr1_r_cr2;
242
243			/* adjust for the granularity of the numbers for angles near 0 or pi */
244
245			if(cos_phi > 1.0) cos_phi = 1.0;
246			if(cos_phi < -1.0) cos_phi = -1.0;
247
248	tim	1742	//cos_phi = dot (A, B) / (rA * rB);
249			//if (cos_phi > 1.0) {
250			// cos_phi = 1.0;
251			//}
252			//if (cos_phi < -1.0) {
253			// cos_phi = -1.0;
254			//}
255	tim	1692
256	tim	1742
257
258	tim	1692	/********************************************************************
259			*
260			* This next section calculates derivatives needed for the force
261			* calculation
262			*
263			********************************************************************/
264
265
266			/* the derivatives of cos phi with respect to the x, y,
267			and z components of vectors cr1 and cr2. */
268			double d_cos_dx_cr1;
269			double d_cos_dy_cr1;
270			double d_cos_dz_cr1;
271			double d_cos_dx_cr2;
272			double d_cos_dy_cr2;
273			double d_cos_dz_cr2;
274
275			d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr;
276			d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr;
277			d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr;
278
279			d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr;
280			d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr;
281			d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr;
282
283	tim	1742	//Vector3d dcosdA = B /(rA * rB) - cos_phi /(rA * rA) * A;
284			//Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize());
285			//Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize());
286
287	tim	1692	/***********************************************************************
288			*
289			* Calculate the actual forces and place them in the atoms.
290			*
291			***********************************************************************/
292
293			double force; /the force scaling factor /
294
295			force = torsion_force(cos_phi);
296
297			aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y);
298			aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z);
299			aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x);
300
301			bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z)
302	tim	1742	- d_cos_dy_cr2 * r_cd.z
303			+ d_cos_dz_cr1 * (r_cb.y - r_ab.y)
304			+ d_cos_dz_cr2 * r_cd.y);
305	tim	1692	bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z)
306	tim	1742	+ d_cos_dx_cr2 * r_cd.z
307			+ d_cos_dz_cr1 * (r_ab.x - r_cb.x)
308			- d_cos_dz_cr2 * r_cd.x);
309	tim	1692	bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y)
310	tim	1742	- d_cos_dx_cr2 * r_cd.y
311			+ d_cos_dy_cr1 * (r_cb.x - r_ab.x)
312			+ d_cos_dy_cr2 * r_cd.x);
313	tim	1692
314			cF[0] = force * (- d_cos_dy_cr1 * r_ab.z
315	tim	1742	- d_cos_dy_cr2 * (r_cb.z - r_cd.z)
316			+ d_cos_dz_cr1 * r_ab.y
317			- d_cos_dz_cr2 * (r_cd.y - r_cb.y));
318	tim	1692	cF[1] = force * ( d_cos_dx_cr1 * r_ab.z
319	tim	1742	- d_cos_dx_cr2 * (r_cd.z - r_cb.z)
320			- d_cos_dz_cr1 * r_ab.x
321			- d_cos_dz_cr2 * (r_cb.x - r_cd.x));
322	tim	1692	cF[2] = force * (- d_cos_dx_cr1 * r_ab.y
323	tim	1742	- d_cos_dx_cr2 * (r_cb.y - r_cd.y)
324			+ d_cos_dy_cr1 * r_ab.x
325			- d_cos_dy_cr2 * (r_cd.x - r_cb.x));
326	tim	1692
327			dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y);
328			dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z);
329			dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x);
330
331
332			c_p_a->addFrc(aF);
333			c_p_b->addFrc(bF);
334			c_p_c->addFrc(cF);
335			c_p_d->addFrc(dF);
336	tim	1742
337			//double firstDerivative;
338			//bondType_->calcForce(cos_phi, firstDerivative, potential_);
339			//f1 = force * cross (dcosdA, r32);
340			//f2 =
341			//f3 =
342			//f4 = force * cross(dcosdB, r32);
343			//atom1_->addFrc(f1);
344			//atom2_->addFrc(f2);
345			//atom3_->addFrc(f3);
346			//atom4_->addFrc(f4);
347
348
349	tim	1692	}
350	tim	1742
351			}