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#include "primitives/SRI.hpp" |
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#include "primitives/Atom.hpp" |
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#include <math.h> |
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#include <iostream> |
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#include <stdlib.h> |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "primitives/Torsion.hpp" |
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|
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void Torsion::set_atoms( Atom &a, Atom &b, Atom &c, Atom &d){ |
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c_p_a = &a; |
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c_p_b = &b; |
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c_p_c = &c; |
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c_p_d = &d; |
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} |
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namespace oopse { |
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|
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Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
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TorsionType *tt) : |
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atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { } |
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void Torsion::calc_forces(){ |
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|
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/********************************************************************** |
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* |
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* initialize vectors |
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* |
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***********************************************************************/ |
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|
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vect r_ab; /* the vector whose origin is a and end is b */ |
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vect r_cb; /* the vector whose origin is c and end is b */ |
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vect r_cd; /* the vector whose origin is c and end is b */ |
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vect r_cr1; /* the cross product of r_ab and r_cb */ |
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vect r_cr2; /* the cross product of r_cb and r_cd */ |
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void Torsion::calcForce() { |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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Vector3d pos4 = atom4_->getPos(); |
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|
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double r_cr1_x2; /* the components of r_cr1 squared */ |
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double r_cr1_y2; |
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double r_cr1_z2; |
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|
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double r_cr2_x2; /* the components of r_cr2 squared */ |
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double r_cr2_y2; |
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double r_cr2_z2; |
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Vector3d r21 = pos1 - pos2; |
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Vector3d r32 = pos2 - pos3; |
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Vector3d r43 = pos3 - pos4; |
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|
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double r_cr1_sqr; /* the length of r_cr1 squared */ |
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double r_cr2_sqr; /* the length of r_cr2 squared */ |
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|
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double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */ |
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|
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double aR[3], bR[3], cR[3], dR[3]; |
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double aF[3], bF[3], cF[3], dF[3]; |
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// Calculate the cross products and distances |
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Vector3d A = cross(r21, r32); |
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double rA = A.length(); |
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Vector3d B = cross(r32, r43); |
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double rB = B.length(); |
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Vector3d C = cross(r32, A); |
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double rC = C.length(); |
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|
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c_p_a->getPos( aR ); |
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c_p_b->getPos( bR ); |
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c_p_c->getPos( cR ); |
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c_p_d->getPos( dR ); |
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A.normalize(); |
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B.normalize(); |
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C.normalize(); |
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|
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// Calculate the sin and cos |
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double cos_phi = dot(A, B) ; |
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double sin_phi = dot(C, B); |
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r_ab.x = bR[0] - aR[0]; |
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r_ab.y = bR[1] - aR[1]; |
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r_ab.z = bR[2] - aR[2]; |
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r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
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double dVdPhi; |
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torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
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r_cb.x = bR[0] - cR[0]; |
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r_cb.y = bR[1] - cR[1]; |
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r_cb.z = bR[2] - cR[2]; |
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r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z)); |
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Vector3d f1; |
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Vector3d f2; |
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Vector3d f3; |
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r_cd.x = dR[0] - cR[0]; |
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r_cd.y = dR[1] - cR[1]; |
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r_cd.z = dR[2] - cR[2]; |
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r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z)); |
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// Next, we want to calculate the forces. In order |
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// to do that, we first need to figure out whether the |
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// sin or cos form will be more stable. For this, |
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// just look at the value of phi |
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//if (fabs(sin_phi) > 0.1) { |
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// use the sin version to avoid 1/cos terms |
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r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z; |
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r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x; |
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r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y; |
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r_cr1_x2 = r_cr1.x * r_cr1.x; |
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r_cr1_y2 = r_cr1.y * r_cr1.y; |
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r_cr1_z2 = r_cr1.z * r_cr1.z; |
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r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2; |
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r_cr1.length = sqrt(r_cr1_sqr); |
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Vector3d dcosdA = (cos_phi * A - B) /rA; |
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Vector3d dcosdB = (cos_phi * B - A) /rB; |
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r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z; |
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r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x; |
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r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y; |
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r_cr2_x2 = r_cr2.x * r_cr2.x; |
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r_cr2_y2 = r_cr2.y * r_cr2.y; |
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r_cr2_z2 = r_cr2.z * r_cr2.z; |
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r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2; |
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r_cr2.length = sqrt(r_cr2_sqr); |
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double dVdcosPhi = -dVdPhi / sin_phi; |
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r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
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f1 = dVdcosPhi * cross(r32, dcosdA); |
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f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
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f3 = dVdcosPhi * cross(dcosdB, r32); |
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/********************************************************************** |
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* |
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* dot product and angle calculations |
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* |
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***********************************************************************/ |
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|
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double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */ |
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double cos_phi; /* the cosine of the torsion angle */ |
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/** @todo fix below block, must be something wrong with the sign somewhere */ |
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//} else { |
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// This angle is closer to 0 or 180 than it is to |
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// 90, so use the cos version to avoid 1/sin terms |
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cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z; |
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cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
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/* adjust for the granularity of the numbers for angles near 0 or pi */ |
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//double dVdsinPhi = dVdPhi /cos_phi; |
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//Vector3d dsindB = (sin_phi * B - C) /rB; |
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//Vector3d dsindC = (sin_phi * C - B) /rC; |
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if(cos_phi > 1.0) cos_phi = 1.0; |
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if(cos_phi < -1.0) cos_phi = -1.0; |
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//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()); |
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//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()); |
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|
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/******************************************************************** |
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* |
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* This next section calculates derivatives needed for the force |
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* calculation |
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* |
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********************************************************************/ |
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//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()); |
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//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() |
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//+ (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z()); |
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/* the derivatives of cos phi with respect to the x, y, |
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and z components of vectors cr1 and cr2. */ |
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double d_cos_dx_cr1; |
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double d_cos_dy_cr1; |
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double d_cos_dz_cr1; |
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double d_cos_dx_cr2; |
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double d_cos_dy_cr2; |
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double d_cos_dz_cr2; |
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//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() |
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//+ (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x()); |
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|
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d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr; |
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d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr; |
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d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr; |
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//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() |
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//+(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y()); |
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|
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d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr; |
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d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr; |
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d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr; |
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//f3 = dVdsinPhi * cross(r32, dsindB); |
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|
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/*********************************************************************** |
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* |
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* Calculate the actual forces and place them in the atoms. |
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* |
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***********************************************************************/ |
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//} |
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|
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double force; /*the force scaling factor */ |
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atom1_->addFrc(f1); |
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atom2_->addFrc(f2 - f1); |
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atom3_->addFrc(f3 - f2); |
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atom4_->addFrc(-f3); |
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} |
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|
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force = torsion_force(cos_phi); |
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– |
|
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– |
aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y); |
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– |
aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z); |
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– |
aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x); |
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– |
|
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– |
bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z) |
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- d_cos_dy_cr2 * r_cd.z |
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+ d_cos_dz_cr1 * (r_cb.y - r_ab.y) |
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– |
+ d_cos_dz_cr2 * r_cd.y); |
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– |
bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z) |
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+ d_cos_dx_cr2 * r_cd.z |
| 149 |
– |
+ d_cos_dz_cr1 * (r_ab.x - r_cb.x) |
| 150 |
– |
- d_cos_dz_cr2 * r_cd.x); |
| 151 |
– |
bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y) |
| 152 |
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- d_cos_dx_cr2 * r_cd.y |
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+ d_cos_dy_cr1 * (r_cb.x - r_ab.x) |
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– |
+ d_cos_dy_cr2 * r_cd.x); |
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– |
|
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– |
cF[0] = force * (- d_cos_dy_cr1 * r_ab.z |
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- d_cos_dy_cr2 * (r_cb.z - r_cd.z) |
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+ d_cos_dz_cr1 * r_ab.y |
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– |
- d_cos_dz_cr2 * (r_cd.y - r_cb.y)); |
| 160 |
– |
cF[1] = force * ( d_cos_dx_cr1 * r_ab.z |
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– |
- d_cos_dx_cr2 * (r_cd.z - r_cb.z) |
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– |
- d_cos_dz_cr1 * r_ab.x |
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– |
- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
| 164 |
– |
cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
| 165 |
– |
- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
| 166 |
– |
+ d_cos_dy_cr1 * r_ab.x |
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– |
- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
| 168 |
– |
|
| 169 |
– |
dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
| 170 |
– |
dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
| 171 |
– |
dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x); |
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– |
|
| 173 |
– |
|
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– |
c_p_a->addFrc(aF); |
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– |
c_p_b->addFrc(bF); |
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– |
c_p_c->addFrc(cF); |
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– |
c_p_d->addFrc(dF); |
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} |
