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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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#include <algorithm> |
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|
#include <math.h> |
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|
#include "primitives/RigidBody.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "utils/simError.h" |
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< |
#include "math/MatVec3.h" |
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> |
#include "utils/NumericConstant.hpp" |
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> |
namespace oopse { |
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|
|
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< |
RigidBody::RigidBody() : StuntDouble() { |
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objType = OT_RIGIDBODY; |
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< |
is_linear = false; |
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linear_axis = -1; |
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momIntTol = 1e-6; |
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< |
} |
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> |
RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ |
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|
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< |
RigidBody::~RigidBody() { |
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} |
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> |
} |
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|
|
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< |
void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
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> |
void RigidBody::setPrevA(const RotMat3x3d& a) { |
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> |
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
|
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< |
vec3 coords; |
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< |
vec3 euler; |
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< |
mat3x3 Atmp; |
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> |
for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
if (atoms_[i]->isDirectional()) { |
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> |
atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
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> |
} |
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> |
} |
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|
|
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myAtoms.push_back(at); |
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|
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if( !ats->havePosition() ){ |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tAtom %s does not have a position specified.\n" |
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"\tThis means RigidBody cannot set up reference coordinates.\n", |
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ats->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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coords[0] = ats->getPosX(); |
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coords[1] = ats->getPosY(); |
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coords[2] = ats->getPosZ(); |
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|
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< |
refCoords.push_back(coords); |
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< |
|
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< |
if (at->isDirectional()) { |
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> |
|
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> |
void RigidBody::setA(const RotMat3x3d& a) { |
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> |
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
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< |
if( !ats->haveOrientation() ){ |
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< |
sprintf( painCave.errMsg, |
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< |
"RigidBody error.\n" |
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< |
"\tAtom %s does not have an orientation specified.\n" |
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< |
"\tThis means RigidBody cannot set up reference orientations.\n", |
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< |
ats->getType() ); |
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< |
painCave.isFatal = 1; |
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< |
simError(); |
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< |
} |
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> |
for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
if (atoms_[i]->isDirectional()) { |
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> |
atoms_[i]->setA(refOrients_[i].transpose() * a); |
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> |
} |
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> |
} |
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> |
} |
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|
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< |
euler[0] = ats->getEulerPhi(); |
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< |
euler[1] = ats->getEulerTheta(); |
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< |
euler[2] = ats->getEulerPsi(); |
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|
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< |
doEulerToRotMat(euler, Atmp); |
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< |
|
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refOrients.push_back(Atmp); |
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< |
|
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} |
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} |
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> |
void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
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> |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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> |
//((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
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|
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< |
void RigidBody::getPos(double theP[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theP[i] = pos[i]; |
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} |
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> |
for (int i =0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
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} |
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} |
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|
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< |
void RigidBody::setPos(double theP[3]){ |
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for (int i = 0; i < 3 ; i++) |
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pos[i] = theP[i]; |
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} |
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} |
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|
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< |
void RigidBody::getVel(double theV[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theV[i] = vel[i]; |
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} |
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> |
Mat3x3d RigidBody::getI() { |
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> |
return inertiaTensor_; |
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} |
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|
|
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< |
void RigidBody::setVel(double theV[3]){ |
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for (int i = 0; i < 3 ; i++) |
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< |
vel[i] = theV[i]; |
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} |
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std::vector<RealType> RigidBody::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 RigidBody::getFrc(double theF[3]){ |
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for (int i = 0; i < 3 ; i++) |
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theF[i] = frc[i]; |
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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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< |
void RigidBody::addFrc(double theF[3]){ |
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< |
for (int i = 0; i < 3 ; i++) |
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< |
frc[i] += theF[i]; |
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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 RigidBody::zeroForces() { |
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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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for (int i = 0; i < 3; i++) { |
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frc[i] = 0.0; |
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trq[i] = 0.0; |
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} |
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// get unit vectors along the phi, theta and psi rotation axes |
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|
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< |
} |
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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 RigidBody::setEuler( double phi, double theta, double psi ){ |
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|
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A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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A[0][2] = sin(theta) * sin(psi); |
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|
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A[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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A[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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A[1][2] = sin(theta) * cos(psi); |
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< |
|
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< |
A[2][0] = sin(phi) * sin(theta); |
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< |
A[2][1] = -cos(phi) * sin(theta); |
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< |
A[2][2] = cos(theta); |
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> |
etheta[0] = cphi; |
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> |
etheta[1] = sphi; |
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> |
etheta[2] = 0.0; |
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|
|
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< |
} |
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> |
epsi[0] = stheta * cphi; |
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> |
epsi[1] = stheta * sphi; |
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> |
epsi[2] = ctheta; |
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|
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< |
void RigidBody::getQ( double q[4] ){ |
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< |
|
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< |
double t, s; |
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< |
double ad1, ad2, ad3; |
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< |
|
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< |
t = A[0][0] + A[1][1] + A[2][2] + 1.0; |
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< |
if( t > 0.0 ){ |
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< |
|
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< |
s = 0.5 / sqrt( t ); |
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< |
q[0] = 0.25 / s; |
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< |
q[1] = (A[1][2] - A[2][1]) * s; |
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< |
q[2] = (A[2][0] - A[0][2]) * s; |
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< |
q[3] = (A[0][1] - A[1][0]) * s; |
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< |
} |
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< |
else{ |
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< |
|
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< |
ad1 = fabs( A[0][0] ); |
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< |
ad2 = fabs( A[1][1] ); |
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< |
ad3 = fabs( A[2][2] ); |
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< |
|
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< |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
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< |
|
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< |
s = 2.0 * sqrt( 1.0 + A[0][0] - A[1][1] - A[2][2] ); |
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< |
q[0] = (A[1][2] + A[2][1]) / s; |
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< |
q[1] = 0.5 / s; |
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< |
q[2] = (A[0][1] + A[1][0]) / s; |
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< |
q[3] = (A[0][2] + A[2][0]) / s; |
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< |
} |
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< |
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
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< |
|
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< |
s = sqrt( 1.0 + A[1][1] - A[0][0] - A[2][2] ) * 2.0; |
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< |
q[0] = (A[0][2] + A[2][0]) / s; |
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< |
q[1] = (A[0][1] + A[1][0]) / s; |
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< |
q[2] = 0.5 / s; |
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< |
q[3] = (A[1][2] + A[2][1]) / s; |
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< |
} |
| 155 |
< |
else{ |
| 156 |
< |
|
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< |
s = sqrt( 1.0 + A[2][2] - A[0][0] - A[1][1] ) * 2.0; |
| 158 |
< |
q[0] = (A[0][1] + A[1][0]) / s; |
| 159 |
< |
q[1] = (A[0][2] + A[2][0]) / s; |
| 160 |
< |
q[2] = (A[1][2] + A[2][1]) / s; |
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< |
q[3] = 0.5 / s; |
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< |
} |
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< |
} |
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< |
} |
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> |
//gradient is equal to -force |
| 129 |
> |
for (int j = 0 ; j<3; j++) |
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> |
grad[j] = -force[j]; |
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|
|
| 132 |
< |
void RigidBody::setQ( double the_q[4] ){ |
| 132 |
> |
for (int j = 0; j < 3; j++ ) { |
| 133 |
|
|
| 134 |
< |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
| 135 |
< |
|
| 136 |
< |
q0Sqr = the_q[0] * the_q[0]; |
| 171 |
< |
q1Sqr = the_q[1] * the_q[1]; |
| 172 |
< |
q2Sqr = the_q[2] * the_q[2]; |
| 173 |
< |
q3Sqr = the_q[3] * the_q[3]; |
| 174 |
< |
|
| 175 |
< |
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 176 |
< |
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
| 177 |
< |
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
| 178 |
< |
|
| 179 |
< |
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
| 180 |
< |
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
| 181 |
< |
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
| 182 |
< |
|
| 183 |
< |
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
| 184 |
< |
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
| 185 |
< |
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
| 134 |
> |
grad[3] += torque[j]*ephi[j]; |
| 135 |
> |
grad[4] += torque[j]*etheta[j]; |
| 136 |
> |
grad[5] += torque[j]*epsi[j]; |
| 137 |
|
|
| 138 |
< |
} |
| 138 |
> |
} |
| 139 |
> |
|
| 140 |
> |
return grad; |
| 141 |
> |
} |
| 142 |
|
|
| 143 |
< |
void RigidBody::getA( double the_A[3][3] ){ |
| 144 |
< |
|
| 145 |
< |
for (int i = 0; i < 3; i++) |
| 192 |
< |
for (int j = 0; j < 3; j++) |
| 193 |
< |
the_A[i][j] = A[i][j]; |
| 143 |
> |
void RigidBody::accept(BaseVisitor* v) { |
| 144 |
> |
v->visit(this); |
| 145 |
> |
} |
| 146 |
|
|
| 147 |
< |
} |
| 147 |
> |
/**@todo need modification */ |
| 148 |
> |
void RigidBody::calcRefCoords() { |
| 149 |
> |
RealType mtmp; |
| 150 |
> |
Vector3d refCOM(0.0); |
| 151 |
> |
mass_ = 0.0; |
| 152 |
> |
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 153 |
> |
mtmp = atoms_[i]->getMass(); |
| 154 |
> |
mass_ += mtmp; |
| 155 |
> |
refCOM += refCoords_[i]*mtmp; |
| 156 |
> |
} |
| 157 |
> |
refCOM /= mass_; |
| 158 |
|
|
| 159 |
< |
void RigidBody::setA( double the_A[3][3] ){ |
| 159 |
> |
// Next, move the origin of the reference coordinate system to the COM: |
| 160 |
> |
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 161 |
> |
refCoords_[i] -= refCOM; |
| 162 |
> |
} |
| 163 |
|
|
| 164 |
< |
for (int i = 0; i < 3; i++) |
| 165 |
< |
for (int j = 0; j < 3; j++) |
| 166 |
< |
A[i][j] = the_A[i][j]; |
| 167 |
< |
|
| 168 |
< |
} |
| 169 |
< |
|
| 170 |
< |
void RigidBody::getJ( double theJ[3] ){ |
| 171 |
< |
|
| 172 |
< |
for (int i = 0; i < 3; i++) |
| 173 |
< |
theJ[i] = ji[i]; |
| 164 |
> |
// Moment of Inertia calculation |
| 165 |
> |
Mat3x3d Itmp(0.0); |
| 166 |
> |
for (std::size_t i = 0; i < atoms_.size(); i++) { |
| 167 |
> |
Mat3x3d IAtom(0.0); |
| 168 |
> |
mtmp = atoms_[i]->getMass(); |
| 169 |
> |
IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
| 170 |
> |
RealType r2 = refCoords_[i].lengthSquare(); |
| 171 |
> |
IAtom(0, 0) += mtmp * r2; |
| 172 |
> |
IAtom(1, 1) += mtmp * r2; |
| 173 |
> |
IAtom(2, 2) += mtmp * r2; |
| 174 |
> |
Itmp += IAtom; |
| 175 |
|
|
| 176 |
< |
} |
| 176 |
> |
//project the inertial moment of directional atoms into this rigid body |
| 177 |
> |
if (atoms_[i]->isDirectional()) { |
| 178 |
> |
Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
|
|
| 182 |
< |
void RigidBody::setJ( double theJ[3] ){ |
| 182 |
> |
// std::cout << Itmp << std::endl; |
| 183 |
> |
|
| 184 |
> |
//diagonalize |
| 185 |
> |
Vector3d evals; |
| 186 |
> |
Mat3x3d::diagonalize(Itmp, evals, sU_); |
| 187 |
> |
|
| 188 |
> |
// zero out I and then fill the diagonals with the moments of inertia: |
| 189 |
> |
inertiaTensor_(0, 0) = evals[0]; |
| 190 |
> |
inertiaTensor_(1, 1) = evals[1]; |
| 191 |
> |
inertiaTensor_(2, 2) = evals[2]; |
| 192 |
> |
|
| 193 |
> |
int nLinearAxis = 0; |
| 194 |
> |
for (int i = 0; i < 3; i++) { |
| 195 |
> |
if (fabs(evals[i]) < oopse::epsilon) { |
| 196 |
> |
linear_ = true; |
| 197 |
> |
linearAxis_ = i; |
| 198 |
> |
++ nLinearAxis; |
| 199 |
> |
} |
| 200 |
> |
} |
| 201 |
> |
|
| 202 |
> |
if (nLinearAxis > 1) { |
| 203 |
> |
sprintf( painCave.errMsg, |
| 204 |
> |
"RigidBody error.\n" |
| 205 |
> |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 206 |
> |
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 207 |
> |
"\t 1) Only one atom was specified, or \n" |
| 208 |
> |
"\t 2) All atoms were specified at the same location, or\n" |
| 209 |
> |
"\t 3) The programmers did something stupid.\n" |
| 210 |
> |
"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
| 211 |
> |
); |
| 212 |
> |
painCave.isFatal = 1; |
| 213 |
> |
simError(); |
| 214 |
> |
} |
| 215 |
|
|
| 216 |
< |
for (int i = 0; i < 3; i++) |
| 215 |
< |
ji[i] = theJ[i]; |
| 216 |
> |
} |
| 217 |
|
|
| 218 |
< |
} |
| 218 |
> |
void RigidBody::calcForcesAndTorques() { |
| 219 |
> |
Vector3d afrc; |
| 220 |
> |
Vector3d atrq; |
| 221 |
> |
Vector3d apos; |
| 222 |
> |
Vector3d rpos; |
| 223 |
> |
Vector3d frc(0.0); |
| 224 |
> |
Vector3d trq(0.0); |
| 225 |
> |
Vector3d pos = this->getPos(); |
| 226 |
> |
for (int i = 0; i < atoms_.size(); i++) { |
| 227 |
|
|
| 228 |
< |
void RigidBody::getTrq(double theT[3]){ |
| 229 |
< |
for (int i = 0; i < 3 ; i++) |
| 230 |
< |
theT[i] = trq[i]; |
| 231 |
< |
} |
| 228 |
> |
afrc = atoms_[i]->getFrc(); |
| 229 |
> |
apos = atoms_[i]->getPos(); |
| 230 |
> |
rpos = apos - pos; |
| 231 |
> |
|
| 232 |
> |
frc += afrc; |
| 233 |
|
|
| 234 |
< |
void RigidBody::addTrq(double theT[3]){ |
| 235 |
< |
for (int i = 0; i < 3 ; i++) |
| 236 |
< |
trq[i] += theT[i]; |
| 227 |
< |
} |
| 234 |
> |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 235 |
> |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 236 |
> |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 237 |
|
|
| 238 |
< |
void RigidBody::getI( double the_I[3][3] ){ |
| 238 |
> |
// If the atom has a torque associated with it, then we also need to |
| 239 |
> |
// migrate the torques onto the center of mass: |
| 240 |
|
|
| 241 |
< |
for (int i = 0; i < 3; i++) |
| 242 |
< |
for (int j = 0; j < 3; j++) |
| 243 |
< |
the_I[i][j] = I[i][j]; |
| 241 |
> |
if (atoms_[i]->isDirectional()) { |
| 242 |
> |
atrq = atoms_[i]->getTrq(); |
| 243 |
> |
trq += atrq; |
| 244 |
> |
} |
| 245 |
> |
} |
| 246 |
> |
addFrc(frc); |
| 247 |
> |
addTrq(trq); |
| 248 |
> |
} |
| 249 |
|
|
| 250 |
< |
} |
| 250 |
> |
Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
| 251 |
> |
Vector3d afrc; |
| 252 |
> |
Vector3d atrq; |
| 253 |
> |
Vector3d apos; |
| 254 |
> |
Vector3d rpos; |
| 255 |
> |
Vector3d frc(0.0); |
| 256 |
> |
Vector3d trq(0.0); |
| 257 |
> |
Vector3d pos = this->getPos(); |
| 258 |
> |
Mat3x3d tau_(0.0); |
| 259 |
|
|
| 260 |
< |
void RigidBody::lab2Body( double r[3] ){ |
| 260 |
> |
for (int i = 0; i < atoms_.size(); i++) { |
| 261 |
|
|
| 262 |
< |
double rl[3]; // the lab frame vector |
| 262 |
> |
afrc = atoms_[i]->getFrc(); |
| 263 |
> |
apos = atoms_[i]->getPos(); |
| 264 |
> |
rpos = apos - pos; |
| 265 |
> |
|
| 266 |
> |
frc += afrc; |
| 267 |
> |
|
| 268 |
> |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 269 |
> |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 270 |
> |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 271 |
> |
|
| 272 |
> |
// If the atom has a torque associated with it, then we also need to |
| 273 |
> |
// migrate the torques onto the center of mass: |
| 274 |
> |
|
| 275 |
> |
if (atoms_[i]->isDirectional()) { |
| 276 |
> |
atrq = atoms_[i]->getTrq(); |
| 277 |
> |
trq += atrq; |
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
tau_(0,0) -= rpos[0]*afrc[0]; |
| 281 |
> |
tau_(0,1) -= rpos[0]*afrc[1]; |
| 282 |
> |
tau_(0,2) -= rpos[0]*afrc[2]; |
| 283 |
> |
tau_(1,0) -= rpos[1]*afrc[0]; |
| 284 |
> |
tau_(1,1) -= rpos[1]*afrc[1]; |
| 285 |
> |
tau_(1,2) -= rpos[1]*afrc[2]; |
| 286 |
> |
tau_(2,0) -= rpos[2]*afrc[0]; |
| 287 |
> |
tau_(2,1) -= rpos[2]*afrc[1]; |
| 288 |
> |
tau_(2,2) -= rpos[2]*afrc[2]; |
| 289 |
> |
|
| 290 |
> |
} |
| 291 |
> |
addFrc(frc); |
| 292 |
> |
addTrq(trq); |
| 293 |
> |
return tau_; |
| 294 |
> |
} |
| 295 |
> |
|
| 296 |
> |
void RigidBody::updateAtoms() { |
| 297 |
> |
unsigned int i; |
| 298 |
> |
Vector3d ref; |
| 299 |
> |
Vector3d apos; |
| 300 |
> |
DirectionalAtom* dAtom; |
| 301 |
> |
Vector3d pos = getPos(); |
| 302 |
> |
RotMat3x3d a = getA(); |
| 303 |
> |
|
| 304 |
> |
for (i = 0; i < atoms_.size(); i++) { |
| 305 |
> |
|
| 306 |
> |
ref = body2Lab(refCoords_[i]); |
| 307 |
> |
|
| 308 |
> |
apos = pos + ref; |
| 309 |
> |
|
| 310 |
> |
atoms_[i]->setPos(apos); |
| 311 |
> |
|
| 312 |
> |
if (atoms_[i]->isDirectional()) { |
| 313 |
> |
|
| 314 |
> |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 315 |
> |
dAtom->setA(refOrients_[i].transpose() * a); |
| 316 |
> |
} |
| 317 |
> |
|
| 318 |
> |
} |
| 319 |
|
|
| 320 |
< |
rl[0] = r[0]; |
| 242 |
< |
rl[1] = r[1]; |
| 243 |
< |
rl[2] = r[2]; |
| 244 |
< |
|
| 245 |
< |
r[0] = (A[0][0] * rl[0]) + (A[0][1] * rl[1]) + (A[0][2] * rl[2]); |
| 246 |
< |
r[1] = (A[1][0] * rl[0]) + (A[1][1] * rl[1]) + (A[1][2] * rl[2]); |
| 247 |
< |
r[2] = (A[2][0] * rl[0]) + (A[2][1] * rl[1]) + (A[2][2] * rl[2]); |
| 320 |
> |
} |
| 321 |
|
|
| 249 |
– |
} |
| 322 |
|
|
| 323 |
< |
void RigidBody::body2Lab( double r[3] ){ |
| 323 |
> |
void RigidBody::updateAtoms(int frame) { |
| 324 |
> |
unsigned int i; |
| 325 |
> |
Vector3d ref; |
| 326 |
> |
Vector3d apos; |
| 327 |
> |
DirectionalAtom* dAtom; |
| 328 |
> |
Vector3d pos = getPos(frame); |
| 329 |
> |
RotMat3x3d a = getA(frame); |
| 330 |
> |
|
| 331 |
> |
for (i = 0; i < atoms_.size(); i++) { |
| 332 |
> |
|
| 333 |
> |
ref = body2Lab(refCoords_[i], frame); |
| 334 |
|
|
| 335 |
< |
double rb[3]; // the body frame vector |
| 335 |
> |
apos = pos + ref; |
| 336 |
> |
|
| 337 |
> |
atoms_[i]->setPos(apos, frame); |
| 338 |
> |
|
| 339 |
> |
if (atoms_[i]->isDirectional()) { |
| 340 |
> |
|
| 341 |
> |
dAtom = (DirectionalAtom *) atoms_[i]; |
| 342 |
> |
dAtom->setA(refOrients_[i].transpose() * a, frame); |
| 343 |
> |
} |
| 344 |
> |
|
| 345 |
> |
} |
| 346 |
|
|
| 347 |
< |
rb[0] = r[0]; |
| 256 |
< |
rb[1] = r[1]; |
| 257 |
< |
rb[2] = r[2]; |
| 258 |
< |
|
| 259 |
< |
r[0] = (A[0][0] * rb[0]) + (A[1][0] * rb[1]) + (A[2][0] * rb[2]); |
| 260 |
< |
r[1] = (A[0][1] * rb[0]) + (A[1][1] * rb[1]) + (A[2][1] * rb[2]); |
| 261 |
< |
r[2] = (A[0][2] * rb[0]) + (A[1][2] * rb[1]) + (A[2][2] * rb[2]); |
| 347 |
> |
} |
| 348 |
|
|
| 349 |
< |
} |
| 349 |
> |
void RigidBody::updateAtomVel() { |
| 350 |
> |
Mat3x3d skewMat;; |
| 351 |
|
|
| 352 |
< |
double RigidBody::getZangle( ){ |
| 353 |
< |
return zAngle; |
| 267 |
< |
} |
| 352 |
> |
Vector3d ji = getJ(); |
| 353 |
> |
Mat3x3d I = getI(); |
| 354 |
|
|
| 355 |
< |
void RigidBody::setZangle( double zAng ){ |
| 356 |
< |
zAngle = zAng; |
| 357 |
< |
} |
| 355 |
> |
skewMat(0, 0) =0; |
| 356 |
> |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 357 |
> |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 358 |
|
|
| 359 |
< |
void RigidBody::addZangle( double zAng ){ |
| 360 |
< |
zAngle += zAng; |
| 361 |
< |
} |
| 359 |
> |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 360 |
> |
skewMat(1, 1) = 0; |
| 361 |
> |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 362 |
|
|
| 363 |
< |
void RigidBody::calcRefCoords( ) { |
| 363 |
> |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 364 |
> |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 365 |
> |
skewMat(2, 2) = 0; |
| 366 |
|
|
| 367 |
< |
int i,j,k, it, n_linear_coords; |
| 368 |
< |
double mtmp; |
| 281 |
< |
vec3 apos; |
| 282 |
< |
double refCOM[3]; |
| 283 |
< |
vec3 ptmp; |
| 284 |
< |
double Itmp[3][3]; |
| 285 |
< |
double evals[3]; |
| 286 |
< |
double evects[3][3]; |
| 287 |
< |
double r, r2, len; |
| 367 |
> |
Mat3x3d mat = (getA() * skewMat).transpose(); |
| 368 |
> |
Vector3d rbVel = getVel(); |
| 369 |
|
|
| 289 |
– |
// First, find the center of mass: |
| 290 |
– |
|
| 291 |
– |
mass = 0.0; |
| 292 |
– |
for (j=0; j<3; j++) |
| 293 |
– |
refCOM[j] = 0.0; |
| 294 |
– |
|
| 295 |
– |
for (i = 0; i < myAtoms.size(); i++) { |
| 296 |
– |
mtmp = myAtoms[i]->getMass(); |
| 297 |
– |
mass += mtmp; |
| 370 |
|
|
| 371 |
< |
apos = refCoords[i]; |
| 372 |
< |
|
| 373 |
< |
for(j = 0; j < 3; j++) { |
| 374 |
< |
refCOM[j] += apos[j]*mtmp; |
| 375 |
< |
} |
| 371 |
> |
Vector3d velRot; |
| 372 |
> |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 373 |
> |
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 374 |
> |
} |
| 375 |
> |
|
| 376 |
|
} |
| 377 |
< |
|
| 378 |
< |
for(j = 0; j < 3; j++) |
| 379 |
< |
refCOM[j] /= mass; |
| 377 |
> |
|
| 378 |
> |
void RigidBody::updateAtomVel(int frame) { |
| 379 |
> |
Mat3x3d skewMat;; |
| 380 |
|
|
| 381 |
< |
// Next, move the origin of the reference coordinate system to the COM: |
| 381 |
> |
Vector3d ji = getJ(frame); |
| 382 |
> |
Mat3x3d I = getI(); |
| 383 |
|
|
| 384 |
< |
for (i = 0; i < myAtoms.size(); i++) { |
| 385 |
< |
apos = refCoords[i]; |
| 386 |
< |
for (j=0; j < 3; j++) { |
| 314 |
< |
apos[j] = apos[j] - refCOM[j]; |
| 315 |
< |
} |
| 316 |
< |
refCoords[i] = apos; |
| 317 |
< |
} |
| 384 |
> |
skewMat(0, 0) =0; |
| 385 |
> |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 386 |
> |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 387 |
|
|
| 388 |
< |
// Moment of Inertia calculation |
| 388 |
> |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 389 |
> |
skewMat(1, 1) = 0; |
| 390 |
> |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 391 |
|
|
| 392 |
< |
for (i = 0; i < 3; i++) |
| 393 |
< |
for (j = 0; j < 3; j++) |
| 394 |
< |
Itmp[i][j] = 0.0; |
| 324 |
< |
|
| 325 |
< |
for (it = 0; it < myAtoms.size(); it++) { |
| 392 |
> |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 393 |
> |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 394 |
> |
skewMat(2, 2) = 0; |
| 395 |
|
|
| 396 |
< |
mtmp = myAtoms[it]->getMass(); |
| 397 |
< |
ptmp = refCoords[it]; |
| 329 |
< |
r= norm3(ptmp.vec); |
| 330 |
< |
r2 = r*r; |
| 331 |
< |
|
| 332 |
< |
for (i = 0; i < 3; i++) { |
| 333 |
< |
for (j = 0; j < 3; j++) { |
| 334 |
< |
|
| 335 |
< |
if (i==j) Itmp[i][j] += mtmp * r2; |
| 396 |
> |
Mat3x3d mat = (getA(frame) * skewMat).transpose(); |
| 397 |
> |
Vector3d rbVel = getVel(frame); |
| 398 |
|
|
| 399 |
< |
Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j]; |
| 400 |
< |
} |
| 399 |
> |
|
| 400 |
> |
Vector3d velRot; |
| 401 |
> |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 402 |
> |
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 403 |
|
} |
| 404 |
+ |
|
| 405 |
|
} |
| 341 |
– |
|
| 342 |
– |
diagonalize3x3(Itmp, evals, sU); |
| 343 |
– |
|
| 344 |
– |
// zero out I and then fill the diagonals with the moments of inertia: |
| 406 |
|
|
| 407 |
< |
n_linear_coords = 0; |
| 407 |
> |
|
| 408 |
|
|
| 409 |
< |
for (i = 0; i < 3; i++) { |
| 410 |
< |
for (j = 0; j < 3; j++) { |
| 350 |
< |
I[i][j] = 0.0; |
| 351 |
< |
} |
| 352 |
< |
I[i][i] = evals[i]; |
| 409 |
> |
bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
| 410 |
> |
if (index < atoms_.size()) { |
| 411 |
|
|
| 412 |
< |
if (fabs(evals[i]) < momIntTol) { |
| 413 |
< |
is_linear = true; |
| 414 |
< |
n_linear_coords++; |
| 415 |
< |
linear_axis = i; |
| 416 |
< |
} |
| 412 |
> |
Vector3d ref = body2Lab(refCoords_[index]); |
| 413 |
> |
pos = getPos() + ref; |
| 414 |
> |
return true; |
| 415 |
> |
} else { |
| 416 |
> |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 417 |
> |
<< atoms_.size() << "atoms" << std::endl; |
| 418 |
> |
return false; |
| 419 |
> |
} |
| 420 |
|
} |
| 421 |
|
|
| 422 |
< |
if (n_linear_coords > 1) { |
| 423 |
< |
sprintf( painCave.errMsg, |
| 424 |
< |
"RigidBody error.\n" |
| 425 |
< |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 426 |
< |
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 427 |
< |
"\t 1) Only one atom was specified, or \n" |
| 428 |
< |
"\t 2) All atoms were specified at the same location, or\n" |
| 429 |
< |
"\t 3) The programmers did something stupid.\n" |
| 430 |
< |
"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
| 431 |
< |
); |
| 432 |
< |
painCave.isFatal = 1; |
| 433 |
< |
simError(); |
| 373 |
< |
} |
| 374 |
< |
|
| 375 |
< |
// renormalize column vectors: |
| 376 |
< |
|
| 377 |
< |
for (i=0; i < 3; i++) { |
| 378 |
< |
len = 0.0; |
| 379 |
< |
for (j = 0; j < 3; j++) { |
| 380 |
< |
len += sU[i][j]*sU[i][j]; |
| 422 |
> |
bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { |
| 423 |
> |
std::vector<Atom*>::iterator i; |
| 424 |
> |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 425 |
> |
if (i != atoms_.end()) { |
| 426 |
> |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 427 |
> |
Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); |
| 428 |
> |
pos = getPos() + ref; |
| 429 |
> |
return true; |
| 430 |
> |
} else { |
| 431 |
> |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 432 |
> |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 433 |
> |
return false; |
| 434 |
|
} |
| 382 |
– |
len = sqrt(len); |
| 383 |
– |
for (j = 0; j < 3; j++) { |
| 384 |
– |
sU[i][j] /= len; |
| 385 |
– |
} |
| 435 |
|
} |
| 436 |
< |
} |
| 436 |
> |
bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { |
| 437 |
|
|
| 438 |
< |
void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){ |
| 438 |
> |
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
| 439 |
|
|
| 440 |
< |
double phi, theta, psi; |
| 392 |
< |
|
| 393 |
< |
phi = euler[0]; |
| 394 |
< |
theta = euler[1]; |
| 395 |
< |
psi = euler[2]; |
| 396 |
< |
|
| 397 |
< |
myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 398 |
< |
myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 399 |
< |
myA[0][2] = sin(theta) * sin(psi); |
| 400 |
< |
|
| 401 |
< |
myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 402 |
< |
myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 403 |
< |
myA[1][2] = sin(theta) * cos(psi); |
| 404 |
< |
|
| 405 |
< |
myA[2][0] = sin(phi) * sin(theta); |
| 406 |
< |
myA[2][1] = -cos(phi) * sin(theta); |
| 407 |
< |
myA[2][2] = cos(theta); |
| 440 |
> |
if (index < atoms_.size()) { |
| 441 |
|
|
| 442 |
< |
} |
| 442 |
> |
Vector3d velRot; |
| 443 |
> |
Mat3x3d skewMat;; |
| 444 |
> |
Vector3d ref = refCoords_[index]; |
| 445 |
> |
Vector3d ji = getJ(); |
| 446 |
> |
Mat3x3d I = getI(); |
| 447 |
|
|
| 448 |
< |
void RigidBody::calcForcesAndTorques() { |
| 448 |
> |
skewMat(0, 0) =0; |
| 449 |
> |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 450 |
> |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 451 |
|
|
| 452 |
< |
// Convert Atomic forces and torques to total forces and torques: |
| 453 |
< |
int i, j; |
| 454 |
< |
double apos[3]; |
| 416 |
< |
double afrc[3]; |
| 417 |
< |
double atrq[3]; |
| 418 |
< |
double rpos[3]; |
| 452 |
> |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 453 |
> |
skewMat(1, 1) = 0; |
| 454 |
> |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 455 |
|
|
| 456 |
< |
zeroForces(); |
| 457 |
< |
|
| 458 |
< |
for (i = 0; i < myAtoms.size(); i++) { |
| 456 |
> |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 457 |
> |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 458 |
> |
skewMat(2, 2) = 0; |
| 459 |
|
|
| 460 |
< |
myAtoms[i]->getPos(apos); |
| 425 |
< |
myAtoms[i]->getFrc(afrc); |
| 460 |
> |
velRot = (getA() * skewMat).transpose() * ref; |
| 461 |
|
|
| 462 |
< |
for (j=0; j<3; j++) { |
| 463 |
< |
rpos[j] = apos[j] - pos[j]; |
| 464 |
< |
frc[j] += afrc[j]; |
| 462 |
> |
vel =getVel() + velRot; |
| 463 |
> |
return true; |
| 464 |
> |
|
| 465 |
> |
} else { |
| 466 |
> |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 467 |
> |
<< atoms_.size() << "atoms" << std::endl; |
| 468 |
> |
return false; |
| 469 |
|
} |
| 470 |
< |
|
| 432 |
< |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 433 |
< |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 434 |
< |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 470 |
> |
} |
| 471 |
|
|
| 472 |
< |
// If the atom has a torque associated with it, then we also need to |
| 437 |
< |
// migrate the torques onto the center of mass: |
| 472 |
> |
bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { |
| 473 |
|
|
| 474 |
< |
if (myAtoms[i]->isDirectional()) { |
| 474 |
> |
std::vector<Atom*>::iterator i; |
| 475 |
> |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 476 |
> |
if (i != atoms_.end()) { |
| 477 |
> |
return getAtomVel(vel, i - atoms_.begin()); |
| 478 |
> |
} else { |
| 479 |
> |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 480 |
> |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 481 |
> |
return false; |
| 482 |
> |
} |
| 483 |
> |
} |
| 484 |
|
|
| 485 |
< |
myAtoms[i]->getTrq(atrq); |
| 486 |
< |
|
| 487 |
< |
for (j=0; j<3; j++) |
| 488 |
< |
trq[j] += atrq[j]; |
| 485 |
> |
bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { |
| 486 |
> |
if (index < atoms_.size()) { |
| 487 |
> |
|
| 488 |
> |
coor = refCoords_[index]; |
| 489 |
> |
return true; |
| 490 |
> |
} else { |
| 491 |
> |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 492 |
> |
<< atoms_.size() << "atoms" << std::endl; |
| 493 |
> |
return false; |
| 494 |
|
} |
| 495 |
+ |
|
| 496 |
|
} |
| 497 |
|
|
| 498 |
< |
// Convert Torque to Body-fixed coordinates: |
| 499 |
< |
// (Actually, on second thought, don't. Integrator does this now.) |
| 500 |
< |
// lab2Body(trq); |
| 498 |
> |
bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { |
| 499 |
> |
std::vector<Atom*>::iterator i; |
| 500 |
> |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 501 |
> |
if (i != atoms_.end()) { |
| 502 |
> |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 503 |
> |
coor = refCoords_[i - atoms_.begin()]; |
| 504 |
> |
return true; |
| 505 |
> |
} else { |
| 506 |
> |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 507 |
> |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 508 |
> |
return false; |
| 509 |
> |
} |
| 510 |
|
|
| 511 |
< |
} |
| 511 |
> |
} |
| 512 |
|
|
| 454 |
– |
void RigidBody::updateAtoms() { |
| 455 |
– |
int i, j; |
| 456 |
– |
vec3 ref; |
| 457 |
– |
double apos[3]; |
| 458 |
– |
DirectionalAtom* dAtom; |
| 459 |
– |
|
| 460 |
– |
for (i = 0; i < myAtoms.size(); i++) { |
| 461 |
– |
|
| 462 |
– |
ref = refCoords[i]; |
| 513 |
|
|
| 514 |
< |
body2Lab(ref.vec); |
| 465 |
< |
|
| 466 |
< |
for (j = 0; j<3; j++) |
| 467 |
< |
apos[j] = pos[j] + ref.vec[j]; |
| 468 |
< |
|
| 469 |
< |
myAtoms[i]->setPos(apos); |
| 470 |
< |
|
| 471 |
< |
if (myAtoms[i]->isDirectional()) { |
| 472 |
< |
|
| 473 |
< |
dAtom = (DirectionalAtom *) myAtoms[i]; |
| 474 |
< |
dAtom->rotateBy( A ); |
| 475 |
< |
|
| 476 |
< |
} |
| 477 |
< |
} |
| 478 |
< |
} |
| 514 |
> |
void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
| 515 |
|
|
| 516 |
< |
void RigidBody::getGrad( double grad[6] ) { |
| 516 |
> |
Vector3d coords; |
| 517 |
> |
Vector3d euler; |
| 518 |
> |
|
| 519 |
|
|
| 520 |
< |
double myEuler[3]; |
| 521 |
< |
double phi, theta, psi; |
| 522 |
< |
double cphi, sphi, ctheta, stheta; |
| 523 |
< |
double ephi[3]; |
| 524 |
< |
double etheta[3]; |
| 525 |
< |
double epsi[3]; |
| 520 |
> |
atoms_.push_back(at); |
| 521 |
> |
|
| 522 |
> |
if( !ats->havePosition() ){ |
| 523 |
> |
sprintf( painCave.errMsg, |
| 524 |
> |
"RigidBody error.\n" |
| 525 |
> |
"\tAtom %s does not have a position specified.\n" |
| 526 |
> |
"\tThis means RigidBody cannot set up reference coordinates.\n", |
| 527 |
> |
ats->getType().c_str() ); |
| 528 |
> |
painCave.isFatal = 1; |
| 529 |
> |
simError(); |
| 530 |
> |
} |
| 531 |
|
|
| 532 |
< |
this->getEulerAngles(myEuler); |
| 532 |
> |
coords[0] = ats->getPosX(); |
| 533 |
> |
coords[1] = ats->getPosY(); |
| 534 |
> |
coords[2] = ats->getPosZ(); |
| 535 |
|
|
| 536 |
< |
phi = myEuler[0]; |
| 492 |
< |
theta = myEuler[1]; |
| 493 |
< |
psi = myEuler[2]; |
| 536 |
> |
refCoords_.push_back(coords); |
| 537 |
|
|
| 538 |
< |
cphi = cos(phi); |
| 496 |
< |
sphi = sin(phi); |
| 497 |
< |
ctheta = cos(theta); |
| 498 |
< |
stheta = sin(theta); |
| 499 |
< |
|
| 500 |
< |
// get unit vectors along the phi, theta and psi rotation axes |
| 501 |
< |
|
| 502 |
< |
ephi[0] = 0.0; |
| 503 |
< |
ephi[1] = 0.0; |
| 504 |
< |
ephi[2] = 1.0; |
| 505 |
< |
|
| 506 |
< |
etheta[0] = cphi; |
| 507 |
< |
etheta[1] = sphi; |
| 508 |
< |
etheta[2] = 0.0; |
| 538 |
> |
RotMat3x3d identMat = RotMat3x3d::identity(); |
| 539 |
|
|
| 540 |
< |
epsi[0] = stheta * cphi; |
| 511 |
< |
epsi[1] = stheta * sphi; |
| 512 |
< |
epsi[2] = ctheta; |
| 513 |
< |
|
| 514 |
< |
for (int j = 0 ; j<3; j++) |
| 515 |
< |
grad[j] = frc[j]; |
| 540 |
> |
if (at->isDirectional()) { |
| 541 |
|
|
| 542 |
< |
grad[3] = 0.0; |
| 543 |
< |
grad[4] = 0.0; |
| 544 |
< |
grad[5] = 0.0; |
| 545 |
< |
|
| 546 |
< |
for (int j = 0; j < 3; j++ ) { |
| 542 |
> |
if( !ats->haveOrientation() ){ |
| 543 |
> |
sprintf( painCave.errMsg, |
| 544 |
> |
"RigidBody error.\n" |
| 545 |
> |
"\tAtom %s does not have an orientation specified.\n" |
| 546 |
> |
"\tThis means RigidBody cannot set up reference orientations.\n", |
| 547 |
> |
ats->getType().c_str() ); |
| 548 |
> |
painCave.isFatal = 1; |
| 549 |
> |
simError(); |
| 550 |
> |
} |
| 551 |
|
|
| 552 |
< |
grad[3] += trq[j]*ephi[j]; |
| 553 |
< |
grad[4] += trq[j]*etheta[j]; |
| 554 |
< |
grad[5] += trq[j]*epsi[j]; |
| 526 |
< |
|
| 527 |
< |
} |
| 528 |
< |
|
| 529 |
< |
} |
| 552 |
> |
euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0; |
| 553 |
> |
euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0; |
| 554 |
> |
euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0; |
| 555 |
|
|
| 556 |
< |
/** |
| 557 |
< |
* getEulerAngles computes a set of Euler angle values consistent |
| 533 |
< |
* with an input rotation matrix. They are returned in the following |
| 534 |
< |
* order: |
| 535 |
< |
* myEuler[0] = phi; |
| 536 |
< |
* myEuler[1] = theta; |
| 537 |
< |
* myEuler[2] = psi; |
| 538 |
< |
*/ |
| 539 |
< |
void RigidBody::getEulerAngles(double myEuler[3]) { |
| 540 |
< |
|
| 541 |
< |
// We use so-called "x-convention", which is the most common |
| 542 |
< |
// definition. In this convention, the rotation given by Euler |
| 543 |
< |
// angles (phi, theta, psi), where the first rotation is by an angle |
| 544 |
< |
// phi about the z-axis, the second is by an angle theta (0 <= theta |
| 545 |
< |
// <= 180) about the x-axis, and the third is by an angle psi about |
| 546 |
< |
// the z-axis (again). |
| 547 |
< |
|
| 548 |
< |
|
| 549 |
< |
double phi,theta,psi,eps; |
| 550 |
< |
double pi; |
| 551 |
< |
double cphi,ctheta,cpsi; |
| 552 |
< |
double sphi,stheta,spsi; |
| 553 |
< |
double b[3]; |
| 554 |
< |
int flip[3]; |
| 555 |
< |
|
| 556 |
< |
// set the tolerance for Euler angles and rotation elements |
| 557 |
< |
|
| 558 |
< |
eps = 1.0e-8; |
| 559 |
< |
|
| 560 |
< |
theta = acos(min(1.0,max(-1.0,A[2][2]))); |
| 561 |
< |
ctheta = A[2][2]; |
| 562 |
< |
stheta = sqrt(1.0 - ctheta * ctheta); |
| 563 |
< |
|
| 564 |
< |
// when sin(theta) is close to 0, we need to consider the |
| 565 |
< |
// possibility of a singularity. In this case, we can assign an |
| 566 |
< |
// arbitary value to phi (or psi), and then determine the psi (or |
| 567 |
< |
// phi) or vice-versa. We'll assume that phi always gets the |
| 568 |
< |
// rotation, and psi is 0 in cases of singularity. we use atan2 |
| 569 |
< |
// instead of atan, since atan2 will give us -Pi to Pi. Since 0 <= |
| 570 |
< |
// theta <= 180, sin(theta) will be always non-negative. Therefore, |
| 571 |
< |
// it never changes the sign of both of the parameters passed to |
| 572 |
< |
// atan2. |
| 573 |
< |
|
| 574 |
< |
if (fabs(stheta) <= eps){ |
| 575 |
< |
psi = 0.0; |
| 576 |
< |
phi = atan2(-A[1][0], A[0][0]); |
| 577 |
< |
} |
| 578 |
< |
// we only have one unique solution |
| 579 |
< |
else{ |
| 580 |
< |
phi = atan2(A[2][0], -A[2][1]); |
| 581 |
< |
psi = atan2(A[0][2], A[1][2]); |
| 582 |
< |
} |
| 583 |
< |
|
| 584 |
< |
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
| 585 |
< |
//if (phi < 0) |
| 586 |
< |
// phi += M_PI; |
| 587 |
< |
|
| 588 |
< |
//if (psi < 0) |
| 589 |
< |
// psi += M_PI; |
| 590 |
< |
|
| 591 |
< |
myEuler[0] = phi; |
| 592 |
< |
myEuler[1] = theta; |
| 593 |
< |
myEuler[2] = psi; |
| 594 |
< |
|
| 595 |
< |
return; |
| 596 |
< |
} |
| 597 |
< |
|
| 598 |
< |
double RigidBody::max(double x, double y) { |
| 599 |
< |
return (x > y) ? x : y; |
| 600 |
< |
} |
| 601 |
< |
|
| 602 |
< |
double RigidBody::min(double x, double y) { |
| 603 |
< |
return (x > y) ? y : x; |
| 604 |
< |
} |
| 605 |
< |
|
| 606 |
< |
void RigidBody::findCOM() { |
| 607 |
< |
|
| 608 |
< |
size_t i; |
| 609 |
< |
int j; |
| 610 |
< |
double mtmp; |
| 611 |
< |
double ptmp[3]; |
| 612 |
< |
double vtmp[3]; |
| 613 |
< |
|
| 614 |
< |
for(j = 0; j < 3; j++) { |
| 615 |
< |
pos[j] = 0.0; |
| 616 |
< |
vel[j] = 0.0; |
| 617 |
< |
} |
| 618 |
< |
mass = 0.0; |
| 619 |
< |
|
| 620 |
< |
for (i = 0; i < myAtoms.size(); i++) { |
| 556 |
> |
RotMat3x3d Atmp(euler); |
| 557 |
> |
refOrients_.push_back(Atmp); |
| 558 |
|
|
| 559 |
< |
mtmp = myAtoms[i]->getMass(); |
| 560 |
< |
myAtoms[i]->getPos(ptmp); |
| 624 |
< |
myAtoms[i]->getVel(vtmp); |
| 625 |
< |
|
| 626 |
< |
mass += mtmp; |
| 627 |
< |
|
| 628 |
< |
for(j = 0; j < 3; j++) { |
| 629 |
< |
pos[j] += ptmp[j]*mtmp; |
| 630 |
< |
vel[j] += vtmp[j]*mtmp; |
| 559 |
> |
}else { |
| 560 |
> |
refOrients_.push_back(identMat); |
| 561 |
|
} |
| 632 |
– |
|
| 633 |
– |
} |
| 562 |
|
|
| 563 |
< |
for(j = 0; j < 3; j++) { |
| 636 |
< |
pos[j] /= mass; |
| 637 |
< |
vel[j] /= mass; |
| 563 |
> |
|
| 564 |
|
} |
| 565 |
|
|
| 566 |
|
} |
| 567 |
|
|
| 642 |
– |
void RigidBody::accept(BaseVisitor* v){ |
| 643 |
– |
vector<Atom*>::iterator atomIter; |
| 644 |
– |
v->visit(this); |
| 645 |
– |
|
| 646 |
– |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
| 647 |
– |
// (*atomIter)->accept(v); |
| 648 |
– |
} |
| 649 |
– |
void RigidBody::getAtomRefCoor(double pos[3], int index){ |
| 650 |
– |
vec3 ref; |
| 651 |
– |
|
| 652 |
– |
ref = refCoords[index]; |
| 653 |
– |
pos[0] = ref[0]; |
| 654 |
– |
pos[1] = ref[1]; |
| 655 |
– |
pos[2] = ref[2]; |
| 656 |
– |
|
| 657 |
– |
} |
| 658 |
– |
|
| 659 |
– |
|
| 660 |
– |
void RigidBody::getAtomPos(double theP[3], int index){ |
| 661 |
– |
vec3 ref; |
| 662 |
– |
|
| 663 |
– |
if (index >= myAtoms.size()) |
| 664 |
– |
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
| 665 |
– |
|
| 666 |
– |
ref = refCoords[index]; |
| 667 |
– |
body2Lab(ref.vec); |
| 668 |
– |
|
| 669 |
– |
theP[0] = pos[0] + ref[0]; |
| 670 |
– |
theP[1] = pos[1] + ref[1]; |
| 671 |
– |
theP[2] = pos[2] + ref[2]; |
| 672 |
– |
} |
| 673 |
– |
|
| 674 |
– |
|
| 675 |
– |
void RigidBody::getAtomVel(double theV[3], int index){ |
| 676 |
– |
vec3 ref; |
| 677 |
– |
double velRot[3]; |
| 678 |
– |
double skewMat[3][3]; |
| 679 |
– |
double aSkewMat[3][3]; |
| 680 |
– |
double aSkewTransMat[3][3]; |
| 681 |
– |
|
| 682 |
– |
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
| 683 |
– |
|
| 684 |
– |
if (index >= myAtoms.size()) |
| 685 |
– |
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
| 686 |
– |
|
| 687 |
– |
ref = refCoords[index]; |
| 688 |
– |
|
| 689 |
– |
skewMat[0][0] =0; |
| 690 |
– |
skewMat[0][1] = ji[2] /I[2][2]; |
| 691 |
– |
skewMat[0][2] = -ji[1] /I[1][1]; |
| 692 |
– |
|
| 693 |
– |
skewMat[1][0] = -ji[2] /I[2][2]; |
| 694 |
– |
skewMat[1][1] = 0; |
| 695 |
– |
skewMat[1][2] = ji[0]/I[0][0]; |
| 696 |
– |
|
| 697 |
– |
skewMat[2][0] =ji[1] /I[1][1]; |
| 698 |
– |
skewMat[2][1] = -ji[0]/I[0][0]; |
| 699 |
– |
skewMat[2][2] = 0; |
| 700 |
– |
|
| 701 |
– |
matMul3(A, skewMat, aSkewMat); |
| 702 |
– |
|
| 703 |
– |
transposeMat3(aSkewMat, aSkewTransMat); |
| 704 |
– |
|
| 705 |
– |
matVecMul3(aSkewTransMat, ref.vec, velRot); |
| 706 |
– |
theV[0] = vel[0] + velRot[0]; |
| 707 |
– |
theV[1] = vel[1] + velRot[1]; |
| 708 |
– |
theV[2] = vel[2] + velRot[2]; |
| 709 |
– |
} |
| 710 |
– |
|
| 711 |
– |
|
