--- trunk/src/integrators/DLM.cpp 2005/01/25 17:45:23 273 +++ trunk/src/integrators/DLM.cpp 2013/06/16 15:15:42 1879 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -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. @@ -37,15 +28,25 @@ * 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 "DLM.hpp" -namespace oopse { +namespace OpenMD { -void DLM::doRotate(StuntDouble* sd, Vector3d& ji, double dt) { - double dt2 = 0.5 * dt; - double angle; + void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) { + RealType dt2 = 0.5 * dt; + RealType angle; RotMat3x3d A = sd->getA(); Mat3x3d I = sd->getI(); @@ -53,54 +54,53 @@ void DLM::doRotate(StuntDouble* sd, Vector3d& ji, doub // use the angular velocities to propagate the rotation matrix a full time step if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i+1)%3; - int k = (i+2)%3; + int i = sd->linearAxis(); + int j = (i+1)%3; + int k = (i+2)%3; - angle = dt2 * ji[j] / I(j, j); - rotateStep( k, i, angle, ji, A ); + angle = dt2 * ji[j] / I(j, j); + rotateStep( k, i, angle, ji, A ); - angle = dt * ji[k] / I(k, k); - rotateStep( i, j, angle, ji, A); + angle = dt * ji[k] / I(k, k); + rotateStep( i, j, angle, ji, A); - angle = dt2 * ji[j] / I(j, j); - rotateStep( k, i, angle, ji, A ); + angle = dt2 * ji[j] / I(j, j); + rotateStep( k, i, angle, ji, A ); } else { - // rotate about the x-axis - angle = dt2 * ji[0] / I(0, 0); - rotateStep( 1, 2, angle, ji, A ); + // rotate about the x-axis + angle = dt2 * ji[0] / I(0, 0); + rotateStep( 1, 2, angle, ji, A ); - // rotate about the y-axis - angle = dt2 * ji[1] / I(1, 1); - rotateStep( 2, 0, angle, ji, A ); + // rotate about the y-axis + angle = dt2 * ji[1] / I(1, 1); + rotateStep( 2, 0, angle, ji, A ); - // rotate about the z-axis - angle = dt * ji[2] / I(2, 2); - sd->addZangle(angle); - rotateStep( 0, 1, angle, ji, A); + // rotate about the z-axis + angle = dt * ji[2] / I(2, 2); + rotateStep( 0, 1, angle, ji, A); - // rotate about the y-axis - angle = dt2 * ji[1] / I(1, 1); - rotateStep( 2, 0, angle, ji, A ); + // rotate about the y-axis + angle = dt2 * ji[1] / I(1, 1); + rotateStep( 2, 0, angle, ji, A ); - // rotate about the x-axis - angle = dt2 * ji[0] / I(0, 0); - rotateStep( 1, 2, angle, ji, A ); + // rotate about the x-axis + angle = dt2 * ji[0] / I(0, 0); + rotateStep( 1, 2, angle, ji, A ); } sd->setA( A ); -} + } -void DLM::rotateStep(int axes1, int axes2, double angle, Vector3d& ji, RotMat3x3d& A) { + void DLM::rotateStep(int axes1, int axes2, RealType angle, Vector3d& ji, RotMat3x3d& A) { - double sinAngle; - double cosAngle; - double angleSqr; - double angleSqrOver4; - double top, bottom; + RealType sinAngle; + RealType cosAngle; + RealType angleSqr; + RealType angleSqrOver4; + RealType top, bottom; RotMat3x3d tempA(A); // initialize the tempA Vector3d tempJ(0.0); @@ -108,16 +108,19 @@ void DLM::rotateStep(int axes1, int axes2, double angl RotMat3x3d rot = RotMat3x3d::identity(); // initalize rot as a unit matrix // use a small angle aproximation for sin and cosine + + angleSqr = angle * angle; + angleSqrOver4 = angleSqr / 4.0; + top = 1.0 - angleSqrOver4; + bottom = 1.0 + angleSqrOver4; - //angleSqr = angle * angle; - //angleSqrOver4 = angleSqr / 4.0; - //top = 1.0 - angleSqrOver4; - //bottom = 1.0 + angleSqrOver4; + cosAngle = top / bottom; + sinAngle = angle / bottom; + + // or don't use the small angle approximation: + //cosAngle = cos(angle); + //sinAngle = sin(angle); - //cosAngle = top / bottom; - //sinAngle = angle / bottom; - cosAngle = cos(angle); - sinAngle = sin(angle); rot(axes1, axes1) = cosAngle; rot(axes2, axes2) = cosAngle; @@ -127,13 +130,28 @@ void DLM::rotateStep(int axes1, int axes2, double angl // rotate the momentum acoording to: ji[] = rot[][] * ji[] ji = rot * ji; - // rotate the Rotation matrix acording to: - // A[][] = A[][] * transpose(rot[][]) - // transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) + // This code comes from converting an algorithm detailed in + // J. Chem. Phys. 107 (15), pp. 5840-5851 by Dullweber, + // Leimkuhler and McLachlan (DLM) for use in our code. + // In Appendix A, the DLM paper has the change to the rotation + // matrix as: Q = Q * rot.transpose(), but our rotation matrix + // A is actually equivalent to Q.transpose(). This fact can be + // seen on page 5849 of the DLM paper where a lab frame + // dipole \mu_i(t) is expressed in terms of a body-fixed + // reference orientation, \bar{\mu_i} and the rotation matrix, Q: + // \mu_i(t) = Q * \bar{\mu_i} + // Our code computes lab frame vectors from body-fixed reference + // vectors using: + // v_{lab} = A.transpose() * v_{body} + // (See StuntDouble.hpp for confirmation of this fact). + // + // So, using the identity: + // (A * B).transpose() = B.transpose() * A.transpose(), we + // get the equivalent of Q = Q * rot.transpose() for our code to be: - A = rot * A; //? A = A* rot.transpose(); + A = rot * A; -} + } }