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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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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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 |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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 "utils/simError.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(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ |
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|
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> |
namespace OpenMD { |
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> |
|
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> |
RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
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> |
inertiaTensor_(0.0){ |
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} |
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|
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> |
|
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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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for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
|
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> |
for (unsigned 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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> |
|
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} |
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|
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< |
|
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> |
|
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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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for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
for (unsigned 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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> |
|
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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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< |
for (int i =0 ; i < atoms_.size(); ++i){ |
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> |
|
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> |
for (unsigned 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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> |
|
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} |
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|
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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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> |
|
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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 phi, theta; |
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> |
// RealType 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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> |
|
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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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> |
// psi = myEuler[2]; |
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> |
|
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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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> |
|
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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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> |
|
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> |
//etheta[0] = -sphi; |
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> |
//etheta[1] = cphi; |
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> |
//etheta[2] = 0.0; |
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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; |
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|
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> |
etheta[2] = 0.0; |
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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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> |
|
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//gradient is equal to -force |
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for (int j = 0 ; j<3; j++) |
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grad[j] = -force[j]; |
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< |
|
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> |
|
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for (int j = 0; j < 3; j++ ) { |
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< |
|
| 138 |
> |
|
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|
grad[3] += torque[j]*ephi[j]; |
| 140 |
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grad[4] += torque[j]*etheta[j]; |
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grad[5] += torque[j]*epsi[j]; |
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< |
|
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> |
|
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|
} |
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|
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return grad; |
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} |
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< |
|
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> |
|
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|
void RigidBody::accept(BaseVisitor* v) { |
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v->visit(this); |
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|
} |
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refCOM += refCoords_[i]*mtmp; |
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} |
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refCOM /= mass_; |
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< |
|
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> |
|
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|
// Next, move the origin of the reference coordinate system to the COM: |
| 165 |
|
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
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refCoords_[i] -= refCOM; |
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IAtom(1, 1) += mtmp * r2; |
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IAtom(2, 2) += mtmp * r2; |
| 179 |
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Itmp += IAtom; |
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< |
|
| 180 |
> |
|
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//project the inertial moment of directional atoms into this rigid body |
| 182 |
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if (atoms_[i]->isDirectional()) { |
| 183 |
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Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
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|
|
| 198 |
|
int nLinearAxis = 0; |
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|
for (int i = 0; i < 3; i++) { |
| 200 |
< |
if (fabs(evals[i]) < oopse::epsilon) { |
| 200 |
> |
if (fabs(evals[i]) < OpenMD::epsilon) { |
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|
linear_ = true; |
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linearAxis_ = i; |
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++ nLinearAxis; |
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if (nLinearAxis > 1) { |
| 208 |
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sprintf( painCave.errMsg, |
| 209 |
|
"RigidBody error.\n" |
| 210 |
< |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 210 |
> |
"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
| 211 |
|
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 212 |
|
"\t 1) Only one atom was specified, or \n" |
| 213 |
|
"\t 2) All atoms were specified at the same location, or\n" |
| 228 |
|
Vector3d frc(0.0); |
| 229 |
|
Vector3d trq(0.0); |
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|
Vector3d pos = this->getPos(); |
| 231 |
< |
for (int i = 0; i < atoms_.size(); i++) { |
| 231 |
> |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 232 |
|
|
| 233 |
|
afrc = atoms_[i]->getFrc(); |
| 234 |
|
apos = atoms_[i]->getPos(); |
| 257 |
|
Vector3d atrq; |
| 258 |
|
Vector3d apos; |
| 259 |
|
Vector3d rpos; |
| 260 |
+ |
Vector3d dfrc; |
| 261 |
|
Vector3d frc(0.0); |
| 262 |
|
Vector3d trq(0.0); |
| 263 |
|
Vector3d pos = this->getPos(); |
| 264 |
|
Mat3x3d tau_(0.0); |
| 265 |
|
|
| 266 |
< |
for (int i = 0; i < atoms_.size(); i++) { |
| 267 |
< |
|
| 266 |
> |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 267 |
> |
|
| 268 |
|
afrc = atoms_[i]->getFrc(); |
| 269 |
|
apos = atoms_[i]->getPos(); |
| 270 |
|
rpos = apos - pos; |
| 292 |
|
tau_(2,0) -= rpos[2]*afrc[0]; |
| 293 |
|
tau_(2,1) -= rpos[2]*afrc[1]; |
| 294 |
|
tau_(2,2) -= rpos[2]*afrc[2]; |
| 295 |
< |
|
| 296 |
< |
} |
| 295 |
> |
|
| 296 |
> |
} |
| 297 |
|
addFrc(frc); |
| 298 |
|
addTrq(trq); |
| 299 |
|
return tau_; |
| 375 |
|
|
| 376 |
|
|
| 377 |
|
Vector3d velRot; |
| 378 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 378 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 379 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 380 |
|
} |
| 381 |
|
|
| 404 |
|
|
| 405 |
|
|
| 406 |
|
Vector3d velRot; |
| 407 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 407 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 408 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 409 |
|
} |
| 410 |
|
|
