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#include <math.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/DirectionalAtom.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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#include "Atom.hpp" |
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#include "DirectionalAtom.hpp" |
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#include "simError.h" |
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#include "MatVec3.h" |
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DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
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: Atom(dAtomType){ |
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objType_= otDAtom; |
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if (dAtomType->isMultipole()) { |
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electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
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} |
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|
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void DirectionalAtom::zeroForces() { |
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if( hasCoords ){ |
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//check if one of the diagonal inertia tensor of this directional atom is zero |
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int nLinearAxis = 0; |
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Mat3x3d inertiaTensor = getI(); |
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for (int i = 0; i < 3; i++) { |
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if (fabs(inertiaTensor(i, i)) < oopse::epsilon) { |
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linear_ = true; |
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linearAxis_ = i; |
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++ nLinearAxis; |
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} |
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} |
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|
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Atom::zeroForces(); |
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|
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trq[offsetX] = 0.0; |
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trq[offsetY] = 0.0; |
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trq[offsetZ] = 0.0; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to zero frc and trq for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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if (nLinearAxis > 1) { |
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sprintf( painCave.errMsg, |
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"Directional Atom warning.\n" |
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"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
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"\tmoment of inertia."); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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} |
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|
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void DirectionalAtom::setCoords(void){ |
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Mat3x3d DirectionalAtom::getI() { |
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return static_cast<DirectionalAtomType*>(getAtomType())->getI(); |
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} |
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|
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if( myConfig->isAllocated() ){ |
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|
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myConfig->getAtomPointers( index, |
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&pos, |
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&vel, |
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&frc, |
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&trq, |
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&Amat, |
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&mu, |
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&ul); |
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void DirectionalAtom::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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else{ |
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sprintf( painCave.errMsg, |
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"Attempted to set Atom %d coordinates with an unallocated " |
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"SimState object.\n", index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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hasCoords = true; |
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|
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void DirectionalAtom::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
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} |
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|
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void DirectionalAtom::setA( double the_A[3][3] ){ |
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|
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if( hasCoords ){ |
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Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
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Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
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Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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|
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this->updateU(); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set Amat for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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|
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void DirectionalAtom::setI( double the_I[3][3] ){ |
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|
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Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2]; |
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Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2]; |
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Izx = the_I[2][0]; Izy = the_I[2][1]; Izz = the_I[2][2]; |
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} |
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if (atomType_->isMultipole()) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
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} |
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} |
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|
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void DirectionalAtom::setQ( double the_q[4] ){ |
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|
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
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|
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if( hasCoords ){ |
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q0Sqr = the_q[0] * the_q[0]; |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
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q3Sqr = the_q[3] * the_q[3]; |
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|
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|
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Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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|
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Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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|
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Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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|
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this->updateU(); |
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void DirectionalAtom::rotateBy(const RotMat3x3d& m) { |
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setA(m *getA()); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set Q for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
|
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} |
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std::vector<RealType> DirectionalAtom::getGrad() { |
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std::vector<RealType> grad(6, 0.0); |
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Vector3d force; |
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Vector3d torque; |
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Vector3d myEuler; |
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RealType phi, theta, psi; |
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RealType cphi, sphi, ctheta, stheta; |
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Vector3d ephi; |
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Vector3d etheta; |
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Vector3d epsi; |
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|
|
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void DirectionalAtom::getA( double the_A[3][3] ){ |
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< |
|
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if( hasCoords ){ |
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< |
the_A[0][0] = Amat[Axx]; |
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the_A[0][1] = Amat[Axy]; |
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the_A[0][2] = Amat[Axz]; |
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|
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the_A[1][0] = Amat[Ayx]; |
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the_A[1][1] = Amat[Ayy]; |
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the_A[1][2] = Amat[Ayz]; |
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< |
|
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the_A[2][0] = Amat[Azx]; |
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the_A[2][1] = Amat[Azy]; |
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< |
the_A[2][2] = Amat[Azz]; |
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< |
} |
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else{ |
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< |
|
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sprintf( painCave.errMsg, |
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"Attempt to get Amat for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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< |
simError(); |
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} |
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force = getFrc(); |
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torque =getTrq(); |
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myEuler = getA().toEulerAngles(); |
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|
|
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< |
} |
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phi = myEuler[0]; |
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theta = myEuler[1]; |
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psi = myEuler[2]; |
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|
|
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< |
void DirectionalAtom::printAmatIndex( void ){ |
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> |
cphi = cos(phi); |
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> |
sphi = sin(phi); |
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> |
ctheta = cos(theta); |
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> |
stheta = sin(theta); |
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|
|
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< |
if( hasCoords ){ |
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< |
std::cerr << "Atom[" << index << "] index =>\n" |
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< |
<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
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< |
<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
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< |
<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
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< |
} |
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< |
else{ |
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< |
|
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< |
sprintf( painCave.errMsg, |
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< |
"Attempt to print Amat indices for atom %d before coords set.\n", |
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< |
index ); |
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< |
painCave.isFatal = 1; |
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< |
simError(); |
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< |
} |
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< |
} |
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> |
// get unit vectors along the phi, theta and psi rotation axes |
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|
|
| 133 |
+ |
ephi[0] = 0.0; |
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+ |
ephi[1] = 0.0; |
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+ |
ephi[2] = 1.0; |
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|
|
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< |
void DirectionalAtom::getU( double the_u[3] ){ |
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< |
|
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< |
the_u[0] = sU[2][0]; |
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< |
the_u[1] = sU[2][1]; |
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< |
the_u[2] = sU[2][2]; |
| 164 |
< |
|
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< |
this->body2Lab( the_u ); |
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< |
} |
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> |
etheta[0] = cphi; |
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> |
etheta[1] = sphi; |
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> |
etheta[2] = 0.0; |
| 140 |
|
|
| 141 |
< |
void DirectionalAtom::getQ( double q[4] ){ |
| 142 |
< |
|
| 143 |
< |
double t, s; |
| 171 |
< |
double ad1, ad2, ad3; |
| 141 |
> |
epsi[0] = stheta * cphi; |
| 142 |
> |
epsi[1] = stheta * sphi; |
| 143 |
> |
epsi[2] = ctheta; |
| 144 |
|
|
| 145 |
< |
if( hasCoords ){ |
| 146 |
< |
|
| 147 |
< |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
| 176 |
< |
if( t > 0.0 ){ |
| 177 |
< |
|
| 178 |
< |
s = 0.5 / sqrt( t ); |
| 179 |
< |
q[0] = 0.25 / s; |
| 180 |
< |
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
| 181 |
< |
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
| 182 |
< |
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
| 183 |
< |
} |
| 184 |
< |
else{ |
| 185 |
< |
|
| 186 |
< |
ad1 = fabs( Amat[Axx] ); |
| 187 |
< |
ad2 = fabs( Amat[Ayy] ); |
| 188 |
< |
ad3 = fabs( Amat[Azz] ); |
| 189 |
< |
|
| 190 |
< |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
| 191 |
< |
|
| 192 |
< |
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
| 193 |
< |
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
| 194 |
< |
q[1] = 0.5 / s; |
| 195 |
< |
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
| 196 |
< |
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
| 197 |
< |
} |
| 198 |
< |
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
| 199 |
< |
|
| 200 |
< |
s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
| 201 |
< |
q[0] = (Amat[Axz] + Amat[Azx]) / s; |
| 202 |
< |
q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
| 203 |
< |
q[2] = 0.5 / s; |
| 204 |
< |
q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
| 205 |
< |
} |
| 206 |
< |
else{ |
| 207 |
< |
|
| 208 |
< |
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
| 209 |
< |
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
| 210 |
< |
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
| 211 |
< |
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
| 212 |
< |
q[3] = 0.5 / s; |
| 213 |
< |
} |
| 214 |
< |
} |
| 215 |
< |
} |
| 216 |
< |
else{ |
| 217 |
< |
|
| 218 |
< |
sprintf( painCave.errMsg, |
| 219 |
< |
"Attempt to get Q for atom %d before coords set.\n", |
| 220 |
< |
index ); |
| 221 |
< |
painCave.isFatal = 1; |
| 222 |
< |
simError(); |
| 223 |
< |
} |
| 224 |
< |
} |
| 145 |
> |
//gradient is equal to -force |
| 146 |
> |
for (int j = 0 ; j<3; j++) |
| 147 |
> |
grad[j] = -force[j]; |
| 148 |
|
|
| 149 |
< |
void DirectionalAtom::setUnitFrameFromEuler(double phi, |
| 227 |
< |
double theta, |
| 228 |
< |
double psi) { |
| 149 |
> |
for (int j = 0; j < 3; j++ ) { |
| 150 |
|
|
| 151 |
< |
double myA[3][3]; |
| 152 |
< |
double uFrame[3][3]; |
| 153 |
< |
double len; |
| 233 |
< |
int i, j; |
| 234 |
< |
|
| 235 |
< |
myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 236 |
< |
myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 237 |
< |
myA[0][2] = sin(theta) * sin(psi); |
| 238 |
< |
|
| 239 |
< |
myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 240 |
< |
myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 241 |
< |
myA[1][2] = sin(theta) * cos(psi); |
| 242 |
< |
|
| 243 |
< |
myA[2][0] = sin(phi) * sin(theta); |
| 244 |
< |
myA[2][1] = -cos(phi) * sin(theta); |
| 245 |
< |
myA[2][2] = cos(theta); |
| 246 |
< |
|
| 247 |
< |
// Make the unit Frame: |
| 151 |
> |
grad[3] -= torque[j]*ephi[j]; |
| 152 |
> |
grad[4] -= torque[j]*etheta[j]; |
| 153 |
> |
grad[5] -= torque[j]*epsi[j]; |
| 154 |
|
|
| 249 |
– |
for (i=0; i < 3; i++) |
| 250 |
– |
for (j=0; j < 3; j++) |
| 251 |
– |
uFrame[i][j] = 0.0; |
| 252 |
– |
|
| 253 |
– |
for (i=0; i < 3; i++) |
| 254 |
– |
uFrame[i][i] = 1.0; |
| 255 |
– |
|
| 256 |
– |
// rotate by the given rotation matrix: |
| 257 |
– |
|
| 258 |
– |
matMul3(myA, uFrame, sU); |
| 259 |
– |
|
| 260 |
– |
// renormalize column vectors: |
| 261 |
– |
|
| 262 |
– |
for (i=0; i < 3; i++) { |
| 263 |
– |
len = 0.0; |
| 264 |
– |
for (j = 0; j < 3; j++) { |
| 265 |
– |
len += sU[i][j]*sU[i][j]; |
| 155 |
|
} |
| 267 |
– |
len = sqrt(len); |
| 268 |
– |
for (j = 0; j < 3; j++) { |
| 269 |
– |
sU[i][j] /= len; |
| 270 |
– |
} |
| 271 |
– |
} |
| 272 |
– |
|
| 273 |
– |
// sU now contains the coordinates of the 'special' frame; |
| 156 |
|
|
| 157 |
< |
} |
| 157 |
> |
return grad; |
| 158 |
> |
} |
| 159 |
|
|
| 160 |
< |
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
| 161 |
< |
|
| 162 |
< |
if( hasCoords ){ |
| 280 |
< |
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 281 |
< |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 282 |
< |
Amat[Axz] = sin(theta) * sin(psi); |
| 283 |
< |
|
| 284 |
< |
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 285 |
< |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 286 |
< |
Amat[Ayz] = sin(theta) * cos(psi); |
| 287 |
< |
|
| 288 |
< |
Amat[Azx] = sin(phi) * sin(theta); |
| 289 |
< |
Amat[Azy] = -cos(phi) * sin(theta); |
| 290 |
< |
Amat[Azz] = cos(theta); |
| 291 |
< |
|
| 292 |
< |
this->updateU(); |
| 293 |
< |
} |
| 294 |
< |
else{ |
| 295 |
< |
|
| 296 |
< |
sprintf( painCave.errMsg, |
| 297 |
< |
"Attempt to set Euler angles for atom %d before coords set.\n", |
| 298 |
< |
index ); |
| 299 |
< |
painCave.isFatal = 1; |
| 300 |
< |
simError(); |
| 301 |
< |
} |
| 302 |
< |
} |
| 160 |
> |
void DirectionalAtom::accept(BaseVisitor* v) { |
| 161 |
> |
v->visit(this); |
| 162 |
> |
} |
| 163 |
|
|
| 304 |
– |
|
| 305 |
– |
void DirectionalAtom::lab2Body( double r[3] ){ |
| 306 |
– |
|
| 307 |
– |
double rl[3]; // the lab frame vector |
| 308 |
– |
|
| 309 |
– |
if( hasCoords ){ |
| 310 |
– |
rl[0] = r[0]; |
| 311 |
– |
rl[1] = r[1]; |
| 312 |
– |
rl[2] = r[2]; |
| 313 |
– |
|
| 314 |
– |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
| 315 |
– |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
| 316 |
– |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
| 317 |
– |
} |
| 318 |
– |
else{ |
| 319 |
– |
|
| 320 |
– |
sprintf( painCave.errMsg, |
| 321 |
– |
"Attempt to convert lab2body for atom %d before coords set.\n", |
| 322 |
– |
index ); |
| 323 |
– |
painCave.isFatal = 1; |
| 324 |
– |
simError(); |
| 325 |
– |
} |
| 326 |
– |
|
| 164 |
|
} |
| 165 |
|
|
| 329 |
– |
void DirectionalAtom::rotateBy( double by_A[3][3]) { |
| 330 |
– |
|
| 331 |
– |
// Check this |
| 332 |
– |
|
| 333 |
– |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 334 |
– |
|
| 335 |
– |
if( hasCoords ){ |
| 336 |
– |
|
| 337 |
– |
r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx]; |
| 338 |
– |
r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy]; |
| 339 |
– |
r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz]; |
| 340 |
– |
|
| 341 |
– |
r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx]; |
| 342 |
– |
r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy]; |
| 343 |
– |
r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz]; |
| 344 |
– |
|
| 345 |
– |
r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx]; |
| 346 |
– |
r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy]; |
| 347 |
– |
r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz]; |
| 348 |
– |
|
| 349 |
– |
Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02; |
| 350 |
– |
Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12; |
| 351 |
– |
Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22; |
| 352 |
– |
|
| 353 |
– |
} |
| 354 |
– |
else{ |
| 355 |
– |
|
| 356 |
– |
sprintf( painCave.errMsg, |
| 357 |
– |
"Attempt to rotate frame for atom %d before coords set.\n", |
| 358 |
– |
index ); |
| 359 |
– |
painCave.isFatal = 1; |
| 360 |
– |
simError(); |
| 361 |
– |
} |
| 362 |
– |
|
| 363 |
– |
} |
| 364 |
– |
|
| 365 |
– |
|
| 366 |
– |
void DirectionalAtom::body2Lab( double r[3] ){ |
| 367 |
– |
|
| 368 |
– |
double rb[3]; // the body frame vector |
| 369 |
– |
|
| 370 |
– |
if( hasCoords ){ |
| 371 |
– |
rb[0] = r[0]; |
| 372 |
– |
rb[1] = r[1]; |
| 373 |
– |
rb[2] = r[2]; |
| 374 |
– |
|
| 375 |
– |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
| 376 |
– |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
| 377 |
– |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
| 378 |
– |
} |
| 379 |
– |
else{ |
| 380 |
– |
|
| 381 |
– |
sprintf( painCave.errMsg, |
| 382 |
– |
"Attempt to convert body2lab for atom %d before coords set.\n", |
| 383 |
– |
index ); |
| 384 |
– |
painCave.isFatal = 1; |
| 385 |
– |
simError(); |
| 386 |
– |
} |
| 387 |
– |
} |
| 388 |
– |
|
| 389 |
– |
void DirectionalAtom::updateU( void ){ |
| 390 |
– |
|
| 391 |
– |
if( hasCoords ){ |
| 392 |
– |
ul[offsetX] = (Amat[Axx] * sU[2][0]) + |
| 393 |
– |
(Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]); |
| 394 |
– |
ul[offsetY] = (Amat[Axy] * sU[2][0]) + |
| 395 |
– |
(Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]); |
| 396 |
– |
ul[offsetZ] = (Amat[Axz] * sU[2][0]) + |
| 397 |
– |
(Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]); |
| 398 |
– |
} |
| 399 |
– |
else{ |
| 400 |
– |
|
| 401 |
– |
sprintf( painCave.errMsg, |
| 402 |
– |
"Attempt to updateU for atom %d before coords set.\n", |
| 403 |
– |
index ); |
| 404 |
– |
painCave.isFatal = 1; |
| 405 |
– |
simError(); |
| 406 |
– |
} |
| 407 |
– |
} |
| 408 |
– |
|
| 409 |
– |
void DirectionalAtom::getJ( double theJ[3] ){ |
| 410 |
– |
|
| 411 |
– |
theJ[0] = jx; |
| 412 |
– |
theJ[1] = jy; |
| 413 |
– |
theJ[2] = jz; |
| 414 |
– |
} |
| 415 |
– |
|
| 416 |
– |
void DirectionalAtom::setJ( double theJ[3] ){ |
| 417 |
– |
|
| 418 |
– |
jx = theJ[0]; |
| 419 |
– |
jy = theJ[1]; |
| 420 |
– |
jz = theJ[2]; |
| 421 |
– |
} |
| 422 |
– |
|
| 423 |
– |
void DirectionalAtom::getTrq( double theT[3] ){ |
| 424 |
– |
|
| 425 |
– |
if( hasCoords ){ |
| 426 |
– |
theT[0] = trq[offsetX]; |
| 427 |
– |
theT[1] = trq[offsetY]; |
| 428 |
– |
theT[2] = trq[offsetZ]; |
| 429 |
– |
} |
| 430 |
– |
else{ |
| 431 |
– |
|
| 432 |
– |
sprintf( painCave.errMsg, |
| 433 |
– |
"Attempt to get Trq for atom %d before coords set.\n", |
| 434 |
– |
index ); |
| 435 |
– |
painCave.isFatal = 1; |
| 436 |
– |
simError(); |
| 437 |
– |
} |
| 438 |
– |
} |
| 439 |
– |
|
| 440 |
– |
void DirectionalAtom::addTrq( double theT[3] ){ |
| 441 |
– |
|
| 442 |
– |
if( hasCoords ){ |
| 443 |
– |
trq[offsetX] += theT[0]; |
| 444 |
– |
trq[offsetY] += theT[1]; |
| 445 |
– |
trq[offsetZ] += theT[2]; |
| 446 |
– |
} |
| 447 |
– |
else{ |
| 448 |
– |
|
| 449 |
– |
sprintf( painCave.errMsg, |
| 450 |
– |
"Attempt to add Trq for atom %d before coords set.\n", |
| 451 |
– |
index ); |
| 452 |
– |
painCave.isFatal = 1; |
| 453 |
– |
simError(); |
| 454 |
– |
} |
| 455 |
– |
} |
| 456 |
– |
|
| 457 |
– |
|
| 458 |
– |
void DirectionalAtom::getI( double the_I[3][3] ){ |
| 459 |
– |
|
| 460 |
– |
the_I[0][0] = Ixx; |
| 461 |
– |
the_I[0][1] = Ixy; |
| 462 |
– |
the_I[0][2] = Ixz; |
| 463 |
– |
|
| 464 |
– |
the_I[1][0] = Iyx; |
| 465 |
– |
the_I[1][1] = Iyy; |
| 466 |
– |
the_I[1][2] = Iyz; |
| 467 |
– |
|
| 468 |
– |
the_I[2][0] = Izx; |
| 469 |
– |
the_I[2][1] = Izy; |
| 470 |
– |
the_I[2][2] = Izz; |
| 471 |
– |
} |
| 472 |
– |
|
| 473 |
– |
void DirectionalAtom::getGrad( double grad[6] ) { |
| 474 |
– |
|
| 475 |
– |
double myEuler[3]; |
| 476 |
– |
double phi, theta, psi; |
| 477 |
– |
double cphi, sphi, ctheta, stheta; |
| 478 |
– |
double ephi[3]; |
| 479 |
– |
double etheta[3]; |
| 480 |
– |
double epsi[3]; |
| 481 |
– |
|
| 482 |
– |
this->getEulerAngles(myEuler); |
| 483 |
– |
|
| 484 |
– |
phi = myEuler[0]; |
| 485 |
– |
theta = myEuler[1]; |
| 486 |
– |
psi = myEuler[2]; |
| 487 |
– |
|
| 488 |
– |
cphi = cos(phi); |
| 489 |
– |
sphi = sin(phi); |
| 490 |
– |
ctheta = cos(theta); |
| 491 |
– |
stheta = sin(theta); |
| 492 |
– |
|
| 493 |
– |
// get unit vectors along the phi, theta and psi rotation axes |
| 494 |
– |
|
| 495 |
– |
ephi[0] = 0.0; |
| 496 |
– |
ephi[1] = 0.0; |
| 497 |
– |
ephi[2] = 1.0; |
| 498 |
– |
|
| 499 |
– |
etheta[0] = cphi; |
| 500 |
– |
etheta[1] = sphi; |
| 501 |
– |
etheta[2] = 0.0; |
| 502 |
– |
|
| 503 |
– |
epsi[0] = stheta * cphi; |
| 504 |
– |
epsi[1] = stheta * sphi; |
| 505 |
– |
epsi[2] = ctheta; |
| 506 |
– |
|
| 507 |
– |
for (int j = 0 ; j<3; j++) |
| 508 |
– |
grad[j] = frc[j]; |
| 509 |
– |
|
| 510 |
– |
grad[3] = 0; |
| 511 |
– |
grad[4] = 0; |
| 512 |
– |
grad[5] = 0; |
| 513 |
– |
|
| 514 |
– |
for (int j = 0; j < 3; j++ ) { |
| 515 |
– |
|
| 516 |
– |
grad[3] += trq[j]*ephi[j]; |
| 517 |
– |
grad[4] += trq[j]*etheta[j]; |
| 518 |
– |
grad[5] += trq[j]*epsi[j]; |
| 519 |
– |
|
| 520 |
– |
} |
| 521 |
– |
|
| 522 |
– |
} |
| 523 |
– |
|
| 524 |
– |
/** |
| 525 |
– |
* getEulerAngles computes a set of Euler angle values consistent |
| 526 |
– |
* with an input rotation matrix. They are returned in the following |
| 527 |
– |
* order: |
| 528 |
– |
* myEuler[0] = phi; |
| 529 |
– |
* myEuler[1] = theta; |
| 530 |
– |
* myEuler[2] = psi; |
| 531 |
– |
*/ |
| 532 |
– |
void DirectionalAtom::getEulerAngles(double myEuler[3]) { |
| 533 |
– |
|
| 534 |
– |
// We use so-called "x-convention", which is the most common definition. |
| 535 |
– |
// In this convention, the rotation given by Euler angles (phi, theta, psi), where the first |
| 536 |
– |
// rotation is by an angle phi about the z-axis, the second is by an angle |
| 537 |
– |
// theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the |
| 538 |
– |
//z-axis (again). |
| 539 |
– |
|
| 540 |
– |
|
| 541 |
– |
double phi,theta,psi,eps; |
| 542 |
– |
double ctheta,stheta; |
| 543 |
– |
|
| 544 |
– |
// set the tolerance for Euler angles and rotation elements |
| 545 |
– |
|
| 546 |
– |
eps = 1.0e-8; |
| 547 |
– |
|
| 548 |
– |
theta = acos(min(1.0,max(-1.0,Amat[Azz]))); |
| 549 |
– |
ctheta = Amat[Azz]; |
| 550 |
– |
stheta = sqrt(1.0 - ctheta * ctheta); |
| 551 |
– |
|
| 552 |
– |
// when sin(theta) is close to 0, we need to consider singularity |
| 553 |
– |
// In this case, we can assign an arbitary value to phi (or psi), and then determine |
| 554 |
– |
// the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0 |
| 555 |
– |
// in cases of singularity. |
| 556 |
– |
// we use atan2 instead of atan, since atan2 will give us -Pi to Pi. |
| 557 |
– |
// Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never |
| 558 |
– |
// change the sign of both of the parameters passed to atan2. |
| 559 |
– |
|
| 560 |
– |
if (fabs(stheta) <= eps){ |
| 561 |
– |
psi = 0.0; |
| 562 |
– |
phi = atan2(-Amat[Ayx], Amat[Axx]); |
| 563 |
– |
} |
| 564 |
– |
// we only have one unique solution |
| 565 |
– |
else{ |
| 566 |
– |
phi = atan2(Amat[Azx], -Amat[Azy]); |
| 567 |
– |
psi = atan2(Amat[Axz], Amat[Ayz]); |
| 568 |
– |
} |
| 569 |
– |
|
| 570 |
– |
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
| 571 |
– |
//if (phi < 0) |
| 572 |
– |
// phi += M_PI; |
| 573 |
– |
|
| 574 |
– |
//if (psi < 0) |
| 575 |
– |
// psi += M_PI; |
| 576 |
– |
|
| 577 |
– |
myEuler[0] = phi; |
| 578 |
– |
myEuler[1] = theta; |
| 579 |
– |
myEuler[2] = psi; |
| 580 |
– |
|
| 581 |
– |
return; |
| 582 |
– |
} |
| 583 |
– |
|
| 584 |
– |
double DirectionalAtom::getZangle( ){ |
| 585 |
– |
|
| 586 |
– |
if( hasCoords ){ |
| 587 |
– |
return zAngle; |
| 588 |
– |
} |
| 589 |
– |
else{ |
| 590 |
– |
|
| 591 |
– |
sprintf( painCave.errMsg, |
| 592 |
– |
"Attempt to get zAngle for atom %d before coords set.\n", |
| 593 |
– |
index ); |
| 594 |
– |
painCave.isFatal = 1; |
| 595 |
– |
simError(); |
| 596 |
– |
return 0; |
| 597 |
– |
} |
| 598 |
– |
} |
| 599 |
– |
|
| 600 |
– |
void DirectionalAtom::setZangle( double zAng ){ |
| 601 |
– |
|
| 602 |
– |
if( hasCoords ){ |
| 603 |
– |
zAngle = zAng; |
| 604 |
– |
} |
| 605 |
– |
else{ |
| 606 |
– |
|
| 607 |
– |
sprintf( painCave.errMsg, |
| 608 |
– |
"Attempt to set zAngle for atom %d before coords set.\n", |
| 609 |
– |
index ); |
| 610 |
– |
painCave.isFatal = 1; |
| 611 |
– |
simError(); |
| 612 |
– |
} |
| 613 |
– |
} |
| 614 |
– |
|
| 615 |
– |
void DirectionalAtom::addZangle( double zAng ){ |
| 616 |
– |
|
| 617 |
– |
if( hasCoords ){ |
| 618 |
– |
zAngle += zAng; |
| 619 |
– |
} |
| 620 |
– |
else{ |
| 621 |
– |
|
| 622 |
– |
sprintf( painCave.errMsg, |
| 623 |
– |
"Attempt to add zAngle to atom %d before coords set.\n", |
| 624 |
– |
index ); |
| 625 |
– |
painCave.isFatal = 1; |
| 626 |
– |
simError(); |
| 627 |
– |
} |
| 628 |
– |
} |
| 629 |
– |
|
| 630 |
– |
double DirectionalAtom::max(double x, double y) { |
| 631 |
– |
return (x > y) ? x : y; |
| 632 |
– |
} |
| 633 |
– |
|
| 634 |
– |
double DirectionalAtom::min(double x, double y) { |
| 635 |
– |
return (x > y) ? y : x; |
| 636 |
– |
} |
