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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/GhostBend.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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namespace oopse { |
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|
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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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#include "utils/simError.h" |
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#include "primitives/SRI.hpp" |
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#include "primitives/Atom.hpp" |
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|
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|
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|
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GhostBend::GhostBend( Atom &a, Atom &b ){ |
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|
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c_p_a = &a; |
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|
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if( !b.isDirectional() ){ |
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/**@todo still a lot left to improve*/ |
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void GhostBend::calcForce() { |
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DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_); |
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|
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// if atom b is not directional, then bad things will happen |
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|
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sprintf( painCave.errMsg, |
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" Ghost Bend error: Atom # %d of type \"%s\" is not " |
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"directional.\n", |
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b.getIndex(), |
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b.getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = ghostAtom->getPos(); |
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|
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atomB = ( DirectionalAtom* ) &b; |
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|
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c_potential_E = 0.0; |
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Vector3d r12 = pos1 - pos2; |
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double d12 = r12.length(); |
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|
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} |
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double d12inv = 1.0 / d12; |
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Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2); |
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double d32 = r32.length(); |
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void GhostBend::calc_forces(){ |
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|
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double dx,dy,dz,gx,gy,gz,dx2,dy2,dz2,gx2,gy2,gz2; |
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double rij2, rkj2, riji2, rkji2, dot, denom, cosang, angl; |
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|
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double sina2, sinai; |
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double d32inv = 1.0 / d32; |
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double comf2, comf3, comf4; |
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double dcsidx, dcsidy, dcsidz, dcskdx, dcskdy, dcskdz; |
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// double dcsjdx, dcsjdy, dcsjdz; |
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double dadxi, dadyi, dadzi; |
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double dadxk, dadyk, dadzk;//, dadxj, dadyj, dadzj; |
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double daxi, dayi, dazi, daxk, dayk, dazk, daxj, dayj, dazj; |
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double u[3]; |
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|
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double aR[3], bR[3]; |
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double aF[3], bF[3], bTrq[3]; |
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double cosTheta = dot(r12, r32) / (d12 * d32); |
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c_p_a->getPos( aR ); |
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atomB->getPos( bR ); |
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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dx = aR[0] - bR[0]; |
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dy = aR[1] - bR[1]; |
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dz = aR[2] - bR[2]; |
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double theta = acos(cosTheta); |
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atomB->getU(u); |
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double firstDerivative; |
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gx = u[0]; |
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gy = u[1]; |
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gz = u[2]; |
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dx2 = dx * dx; |
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dy2 = dy * dy; |
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dz2 = dz * dz; |
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bendType_->calcForce(theta, firstDerivative, potential_); |
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gx2 = gx * gx; |
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gy2 = gy * gy; |
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gz2 = gz * gz; |
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rij2 = dx2 + dy2 + dz2; |
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rkj2 = gx2 + gy2 + gz2; |
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riji2 = 1.0 / rij2; |
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rkji2 = 1.0 / rkj2; |
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double sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
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dot = dx * gx + dy * gy + dz * gz; |
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denom = sqrt((riji2 * rkji2)); |
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cosang = dot * denom; |
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if (fabs(sinTheta) < 1.0E-12) { |
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sinTheta = 1.0E-12; |
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} |
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if(cosang > 1.0)cosang = 1.0; |
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if(cosang < -1.0) cosang = -1.0; |
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double commonFactor1 = -firstDerivative / sinTheta * d12inv; |
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double commonFactor2 = -firstDerivative / sinTheta * d32inv; |
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angl = acos(cosang); |
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angl = angl * 180.0 / M_PI; |
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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
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atom1_->addFrc(force1); |
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ghostAtom->addFrc(-force1); |
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/**@todo test correctness */ |
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ghostAtom->addTrq(cross(r32, force3) ); |
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sina2 = 1.0 - cosang*cosang; |
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if(fabs(sina2) < 1.0E-12 ) sina2 = 1.0E-12; |
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sinai = 1.0 / sqrt(sina2); |
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comf2 = cosang * riji2; |
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comf3 = cosang * rkji2; |
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comf4 = bend_force(angl); |
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dcsidx = gx*denom - comf2*dx; |
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dcsidy = gy*denom - comf2*dy; |
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dcsidz = gz*denom - comf2*dz; |
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dcskdx = dx*denom - comf3*gx; |
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dcskdy = dy*denom - comf3*gy; |
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dcskdz = dz*denom - comf3*gz; |
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|
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// dcsjdx = -dcsidx - dcskdx; |
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// dcsjdy = -dcsidy - dcskdy; |
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// dcsjdz = -dcsidz - dcskdz; |
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dadxi = -sinai*dcsidx; |
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dadyi = -sinai*dcsidy; |
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dadzi = -sinai*dcsidz; |
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dadxk = -sinai*dcskdx; |
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dadyk = -sinai*dcskdy; |
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dadzk = -sinai*dcskdz; |
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|
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// dadxj = -dadxi - dadxk; |
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// dadyj = -dadyi - dadyk; |
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// dadzj = -dadzi - dadzk; |
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|
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daxi = comf4*dadxi; |
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dayi = comf4*dadyi; |
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dazi = comf4*dadzi; |
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|
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daxk = comf4*dadxk; |
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dayk = comf4*dadyk; |
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dazk = comf4*dadzk; |
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|
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daxj = -daxi - daxk; |
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dayj = -dayi - dayk; |
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dazj = -dazi - dazk; |
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|
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aF[0] = daxi; |
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aF[1] = dayi; |
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aF[2] = dazi; |
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bF[0] = daxj + daxk; |
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bF[1] = dayj + dayk; |
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bF[2] = dazj + dazk; |
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|
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bTrq[0] = gy*dazk - gz*dayk; |
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bTrq[1] = gz*daxk - gx*dazk; |
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bTrq[2] = gx*dayk - gy*daxk; |
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c_p_a->addFrc( aF ); |
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atomB->addFrc( bF ); |
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atomB->addTrq( bTrq ); |
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|
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return; |
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} |
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void GhostBend::setConstants( double the_c1, double the_c2, double the_c3, |
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double the_Th0 ){ |
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c1 = the_c1; |
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c2 = the_c2; |
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c3 = the_c3; |
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theta0 = the_Th0; |
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} |
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} //end namespace oopse |
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double GhostBend::bend_force( double theta ){ |
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|
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double dt, dt2; |
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double force; |
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dt = ( theta - theta0 ) * M_PI / 180.0; |
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dt2 = dt * dt; |
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|
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c_potential_E = ( c1 * dt2 ) + ( c2 * dt ) + c3; |
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force = -( ( 2.0 * c1 * dt ) + c2 ); |
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return force; |
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} |
