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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5978 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-04-19 20:57:30 +00:00
parent 99ed989715
commit 105ebaac24
9 changed files with 114 additions and 239 deletions
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77
src/fix_rigid.cpp
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@ -1070,13 +1070,17 @@ void FixRigid::initial_integrate(int vflag)
angmom[ibody][1] += dtf * torque[ibody][1] * tflag[ibody][1];
angmom[ibody][2] += dtf * torque[ibody][2] * tflag[ibody][2];
// update quaternion a full step
// returns new normalized quat
// returns ex_space,ey_space,ez_space for new quat
// returns omega at 1/2 step (depends on angmom and quat)
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion, also updated omega at 1/2 step
// update ex,ey,ez to reflect new quaternion
richardson(quat[ibody],omega[ibody],angmom[ibody],inertia[ibody],
ex_space[ibody],ey_space[ibody],ez_space[ibody]);
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody],
inertia[ibody],dtq);
MathExtra::q_to_exyz(quat[ibody],
ex_space[ibody],ey_space[ibody],ez_space[ibody]);
}
// virial setup before call to set_xv
@ -1199,67 +1203,6 @@ void FixRigid::final_integrate()
set_v();
}
/* ---------------------------------------------------------------------- */
void FixRigid::richardson(double *q, double *w,
double *m, double *moments,
double *ex, double *ey, double *ez)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
MathExtra::angmom_to_omega(m,ex,ey,ez,moments,w);
// full update from dq/dt = 1/2 w q
double wq[4];
MathExtra::vecquat(w,q,wq);
double qfull[4];
qfull[0] = q[0] + dtq * wq[0];
qfull[1] = q[1] + dtq * wq[1];
qfull[2] = q[2] + dtq * wq[2];
qfull[3] = q[3] + dtq * wq[3];
MathExtra::qnormalize(qfull);
// 1st half update from dq/dt = 1/2 w q
double qhalf[4];
qhalf[0] = q[0] + 0.5*dtq * wq[0];
qhalf[1] = q[1] + 0.5*dtq * wq[1];
qhalf[2] = q[2] + 0.5*dtq * wq[2];
qhalf[3] = q[3] + 0.5*dtq * wq[3];
MathExtra::qnormalize(qhalf);
// udpate ex,ey,ez from qhalf
// re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step
// recompute wq
MathExtra::q_to_exyz(qhalf,ex,ey,ez);
MathExtra::angmom_to_omega(m,ex,ey,ez,moments,w);
MathExtra::vecquat(w,qhalf,wq);
// 2nd half update from dq/dt = 1/2 w q
qhalf[0] += 0.5*dtq * wq[0];
qhalf[1] += 0.5*dtq * wq[1];
qhalf[2] += 0.5*dtq * wq[2];
qhalf[3] += 0.5*dtq * wq[3];
MathExtra::qnormalize(qhalf);
// corrected Richardson update
q[0] = 2.0*qhalf[0] - qfull[0];
q[1] = 2.0*qhalf[1] - qfull[1];
q[2] = 2.0*qhalf[2] - qfull[2];
q[3] = 2.0*qhalf[3] - qfull[3];
MathExtra::qnormalize(q);
MathExtra::q_to_exyz(q,ex,ey,ez);
}
/* ----------------------------------------------------------------------
apply evolution operators to quat, quat momentum
see Miller paper cited in fix rigid/nvt and fix rigid/npt