--- trunk/src/primitives/Inversion.cpp 2008/07/04 20:54:29 1275 +++ trunk/src/primitives/Inversion.cpp 2015/03/05 15:35:37 2067 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,77 +28,118 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ +#include "config.h" +#include + #include "primitives/Inversion.hpp" -namespace oopse { +namespace OpenMD { Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, - Atom *atom4, InversionType *it) : - atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), - inversionType_(it) { } + Atom *atom4, InversionType *it) : + ShortRangeInteraction(), inversionType_(it) { + + atoms_.resize(4); + atoms_[0] = atom1; + atoms_[1] = atom2; + atoms_[2] = atom3; + atoms_[3] = atom4; + + inversionKey_ = inversionType_->getKey(); + } - void Inversion::calcForce(RealType& angle) { + void Inversion::calcForce(RealType& angle, bool doParticlePot) { - // In OOPSE's version of an inversion, the central atom + // In OpenMD's version of an inversion, the central atom // comes first. However, to get the planarity in a typical cosine // version of this potential (i.e. Amber-style), the central atom // is treated as atom *3* in a standard torsion form: - Vector3d pos1 = atom2_->getPos(); - Vector3d pos2 = atom3_->getPos(); - Vector3d pos3 = atom1_->getPos(); - Vector3d pos4 = atom4_->getPos(); + Vector3d pos1 = atoms_[1]->getPos(); + Vector3d pos2 = atoms_[2]->getPos(); + Vector3d pos3 = atoms_[0]->getPos(); + Vector3d pos4 = atoms_[3]->getPos(); - Vector3d r21 = pos1 - pos2; - Vector3d r32 = pos2 - pos3; + 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(); A.normalize(); B.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; RealType dVdcosPhi; - inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); - Vector3d f1; - Vector3d f2; - Vector3d f3; + switch (inversionKey_) { + case itCosAngle: + inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); + break; + case itAngle: + RealType phi = acos(cos_phi); + RealType dVdPhi; + inversionType_->calcForce(phi, potential_, dVdPhi); + RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi); + if (fabs(sin_phi) < 1.0E-6) { + sin_phi = 1.0E-6; + } + dVdcosPhi = dVdPhi / sin_phi; + break; + } + + 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 + // In OpenMD's version of an improper torsion, the central atom // comes first. However, to get the planarity in a typical cosine // version of this potential (i.e. Amber-style), the central atom // is treated as atom *3* in a standard torsion form: // AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) - // OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) + // OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon) // Confusing enough? Good. - atom3_->addFrc(f1); - atom1_->addFrc(f2 - f1); - atom2_->addFrc(f3 - f2); - atom4_->addFrc(-f3); + atoms_[1]->addFrc(f1); + atoms_[0]->addFrc(f2 - f1 + f3); + atoms_[3]->addFrc(-f2); + atoms_[2]->addFrc(-f3); + + if (doParticlePot) { + atoms_[0]->addParticlePot(potential_); + atoms_[1]->addParticlePot(potential_); + atoms_[2]->addParticlePot(potential_); + atoms_[3]->addParticlePot(potential_); + } + angle = acos(cos_phi) /M_PI * 180.0; }