--- trunk/src/primitives/Inversion.cpp 2008/07/14 12:35:58 1277 +++ trunk/src/primitives/Inversion.cpp 2008/10/16 18:17:41 1305 @@ -60,40 +60,51 @@ namespace oopse { Vector3d pos3 = atom1_->getPos(); Vector3d pos4 = atom4_->getPos(); - Vector3d r21 = pos1 - pos2; - Vector3d r32 = pos2 - pos3; + /*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 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, r43); + Vector3d B = cross(r43, r23); RealType rB = B.length(); - Vector3d C = cross(r32, A); - RealType rC = C.length(); + //Vector3d C = cross(r23, A); + //RealType rC = C.length(); A.normalize(); B.normalize(); - C.normalize(); + //C.normalize(); // Calculate the sin and cos RealType cos_phi = dot(A, B) ; - if (cos_phi > 1.0) cos_phi = 1.0; - if (cos_phi < -1.0) cos_phi = -1.0; + 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; - RealType dVdcosPhi; + //cos_phi = 2.0*cos_phi*cos_phi - 1.0; inversionType_->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; - f1 = dVdcosPhi * cross(r32, dcosdA); - f2 = dVdcosPhi * ( cross(r43, 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 @@ -105,10 +116,11 @@ namespace oopse { // Confusing enough? Good. - atom3_->addFrc(f1); - atom1_->addFrc(f2 - f1); - atom2_->addFrc(f3 - f2); - atom4_->addFrc(-f3); + atom2_->addFrc(f1); + atom1_->addFrc(f2 - f1 + f3); + atom4_->addFrc(-f2); + atom3_->addFrc(-f3); + angle = acos(cos_phi) /M_PI * 180.0; }