--- trunk/src/primitives/Torsion.cpp	2005/01/12 22:41:40	246
+++ trunk/src/primitives/Torsion.cpp	2008/10/21 18:23:31	1309
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -43,11 +43,12 @@ namespace oopse {
 
 namespace oopse {
 
-Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4,
-                 TorsionType *tt) :
+  Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4,
+		   TorsionType *tt) :
     atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }
 
-void Torsion::calcForce() {
+  void Torsion::calcForce(RealType& angle) {
+
     Vector3d pos1 = atom1_->getPos();
     Vector3d pos2 = atom2_->getPos();
     Vector3d pos3 = atom3_->getPos();
@@ -59,75 +60,45 @@ void Torsion::calcForce() {
 
     //  Calculate the cross products and distances
     Vector3d A = cross(r21, r32);
-    double rA = A.length();
+    RealType rA = A.length();
     Vector3d B = cross(r32, r43);
-    double rB = B.length();
+    RealType rB = B.length();
     Vector3d C = cross(r32, A);
-    double rC = C.length();
+    RealType rC = C.length();
 
     A.normalize();
     B.normalize();
     C.normalize();
     
     //  Calculate the sin and cos
-    double cos_phi = dot(A, B) ;
-    double sin_phi = dot(C, B);
+    RealType cos_phi = dot(A, B) ;
+    if (cos_phi > 1.0) cos_phi = 1.0;
+    if (cos_phi < -1.0) cos_phi = -1.0; 
 
-    double dVdPhi;
-    torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi);
+    RealType dVdcosPhi;
+    torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
+    Vector3d f1 ;
+    Vector3d f2 ;
+    Vector3d f3 ;
 
-    Vector3d f1;
-    Vector3d f2;
-    Vector3d f3;
+    Vector3d dcosdA = (cos_phi * A - B) /rA;
+    Vector3d dcosdB = (cos_phi * B - A) /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
-
-        Vector3d dcosdA = (cos_phi * A - B) /rA;
-        Vector3d dcosdB = (cos_phi * B - A) /rB;
-
-        double dVdcosPhi = -dVdPhi / sin_phi;
-
-        f1 = dVdcosPhi * cross(r32, dcosdA);
-        f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
-        f3 = dVdcosPhi * cross(dcosdB, r32);
-
-    /** @todo fix below block, must be something wrong with the sign somewhere */
-    //} else {
-        //  This angle is closer to 0 or 180 than it is to
-        //  90, so use the cos version to avoid 1/sin terms
-
-        //double dVdsinPhi = dVdPhi /cos_phi;
-        //Vector3d dsindB = (sin_phi * B - C) /rB;
-        //Vector3d dsindC = (sin_phi * C - B) /rC;
-
-        //f1.x() = dVdsinPhi*((r32.y()*r32.y() + r32.z()*r32.z())*dsindC.x() - r32.x()*r32.y()*dsindC.y() - r32.x()*r32.z()*dsindC.z());
-
-        //f1.y() = dVdsinPhi*((r32.z()*r32.z() + r32.x()*r32.x())*dsindC.y() - r32.y()*r32.z()*dsindC.z() - r32.y()*r32.x()*dsindC.x());
-
-        //f1.z() = dVdsinPhi*((r32.x()*r32.x() + r32.y()*r32.y())*dsindC.z() - r32.z()*r32.x()*dsindC.x() - r32.z()*r32.y()*dsindC.y());
-
-        //f2.x() = dVdsinPhi*(-(r32.y()*r21.y() + r32.z()*r21.z())*dsindC.x() + (2.0*r32.x()*r21.y() - r21.x()*r32.y())*dsindC.y()
-        //+ (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z());
-
-        //f2.y() = dVdsinPhi*(-(r32.z()*r21.z() + r32.x()*r21.x())*dsindC.y() + (2.0*r32.y()*r21.z() - r21.y()*r32.z())*dsindC.z()
-        //+ (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x());
-
-        //f2.z() = dVdsinPhi*(-(r32.x()*r21.x() + r32.y()*r21.y())*dsindC.z() + (2.0*r32.z()*r21.x() - r21.z()*r32.x())*dsindC.x()
-        //+(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y());
-
-        //f3 = dVdsinPhi * cross(r32, dsindB);
-
-    //}
-
+    f1 = dVdcosPhi * cross(r32, dcosdA);
+    f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
+    f3 = dVdcosPhi * cross(dcosdB, r32);
+    
     atom1_->addFrc(f1);
     atom2_->addFrc(f2 - f1);
     atom3_->addFrc(f3 - f2);
     atom4_->addFrc(-f3);
-}
 
+    atom1_->addParticlePot(potential_);
+    atom2_->addParticlePot(potential_);
+    atom3_->addParticlePot(potential_);
+    atom4_->addParticlePot(potential_);
+
+    angle = acos(cos_phi) /M_PI * 180.0;
+  }
+
 }