--- trunk/src/primitives/Inversion.cpp	2008/09/10 19:51:45	1290
+++ trunk/src/primitives/Inversion.cpp	2008/10/21 18:23:31	1309
@@ -40,7 +40,6 @@
  */
  
 #include "primitives/Inversion.hpp"
-#include "fstream"
 
 namespace oopse {
 
@@ -57,26 +56,18 @@ namespace oopse {
     // is treated as atom *3* in a standard torsion form:
 
     Vector3d pos1 = atom2_->getPos();
-    Vector3d pos2 = atom1_->getPos();
-    Vector3d pos3 = atom4_->getPos();
-    Vector3d pos4 = atom3_->getPos();
+    Vector3d pos2 = atom3_->getPos();
+    Vector3d pos3 = atom1_->getPos();
+    Vector3d pos4 = atom4_->getPos();
 
-   /*std::ofstream myfile;
-   myfile.open("Inversion", std::ios::app);       
-   myfile << atom1_->getType() << " - atom1; "
-              << atom2_->getType() << " - atom2; "
-              << atom3_->getType() << " - atom3; "
-              << atom4_->getType() << " - atom4; "
-              << std::endl;
-*/
-    Vector3d r21 = pos1 - pos2;
-    Vector3d r32 = pos2 - pos3;
-    Vector3d r42 = pos2 - pos4;
+    Vector3d r31 = pos1 - pos3;
+    Vector3d r23 = pos3 - pos2;
+    Vector3d r43 = pos3 - pos4;
 
     //  Calculate the cross products and distances
-    Vector3d A = cross(r21, r32);
+    Vector3d A = cross(r31, r43);
     RealType rA = A.length();
-    Vector3d B = cross(r32, r42);
+    Vector3d B = cross(r43, r23);
     RealType rB = B.length();
     //Vector3d C = cross(r23, A);
     //RealType rC = C.length();
@@ -87,14 +78,10 @@ namespace oopse {
     
     //  Calculate the sin and cos
     RealType cos_phi = dot(A, B) ;
-    if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" 
-                                                 << std::endl;}
-    if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" 
-                                                   << std::endl;}
-    //std::cout << "We actually use this inversion!!!!" << std::endl;
+    if (cos_phi > 1.0) cos_phi = 1.0;
+    if (cos_phi < -1.0) cos_phi = -1.0;
 
     RealType dVdcosPhi;
-    //cos_phi = 2.0*cos_phi*cos_phi - 1.0;
     inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
     Vector3d f1 ;
     Vector3d f2 ;
@@ -103,9 +90,9 @@ namespace oopse {
     Vector3d dcosdA = (cos_phi * A - B) /rA;
     Vector3d dcosdB = (cos_phi * B - A) /rB;
 
-    f1 = dVdcosPhi * cross(r32, dcosdA);
-    f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA));
-    f3 = dVdcosPhi * cross(dcosdB, r32);
+    f1 = dVdcosPhi * cross(r43, dcosdA);
+    f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
+    f3 = dVdcosPhi * cross(dcosdB, r43);
 
     // In OOPSE's version of an improper torsion, the central atom
     // comes first.  However, to get the planarity in a typical cosine
@@ -122,6 +109,11 @@ namespace oopse {
     atom4_->addFrc(-f2);
     atom3_->addFrc(-f3);
 
+    atom1_->addParticlePot(potential_);
+    atom2_->addParticlePot(potential_);
+    atom3_->addParticlePot(potential_);
+    atom4_->addParticlePot(potential_);
+
     angle = acos(cos_phi) /M_PI * 180.0;
   }