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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2139 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-10-01 22:10:25 +00:00
parent 926394fc45
commit 820f667f2e
2 changed files with 44 additions and 43 deletions
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83
src/fix_rigid.cpp
View File

@ -439,7 +439,7 @@ void FixRigid::init()
ez_space[ibody][0] = evectors[0][2];
ez_space[ibody][1] = evectors[1][2];
ez_space[ibody][2] = evectors[2][2];
// if any principal moment < scaled EPSILON, set to 0.0
double max;
@ -469,7 +469,7 @@ void FixRigid::init()
// create initial quaternion
qcreate(evectors,quat[ibody]);
q_from_exyz(ex_space[ibody],ey_space[ibody],ez_space[ibody],quat[ibody]);
}
// free temporary memory
@ -1111,47 +1111,69 @@ void FixRigid::rotate(double **matrix, int i, int j, int k, int l,
}
/* ----------------------------------------------------------------------
create quaternion from rotation matrix (evectors)
create quaternion from space-frame ex,ey,ez
ex,ey,ez are columns of evectors rotation matrix
------------------------------------------------------------------------- */
void FixRigid::qcreate(double **a, double *q)
void FixRigid::q_from_exyz(double *ex, double *ey, double *ez, double *q)
{
// squares of quaternion components
double q0sq = 0.25 * (a[0][0] + a[1][1] + a[2][2] + 1.0);
double q1sq = q0sq - 0.5 * (a[1][1] + a[2][2]);
double q2sq = q0sq - 0.5 * (a[0][0] + a[2][2]);
double q3sq = q0sq - 0.5 * (a[0][0] + a[1][1]);
double q0sq = 0.25 * (ex[0] + ey[1] + ez[2] + 1.0);
double q1sq = q0sq - 0.5 * (ey[1] + ez[2]);
double q2sq = q0sq - 0.5 * (ex[0] + ez[2]);
double q3sq = q0sq - 0.5 * (ex[0] + ey[1]);
// some component must be greater than 1/4 since they sum to 1
// compute other components from it
if (q0sq >= 0.25) {
q[0] = sqrt(q0sq);
q[1] = (a[2][1] - a[1][2]) / (4.0*q[0]);
q[2] = (a[0][2] - a[2][0]) / (4.0*q[0]);
q[3] = (a[1][0] - a[0][1]) / (4.0*q[0]);
q[1] = (ey[2] - ez[1]) / (4.0*q[0]);
q[2] = (ez[0] - ex[2]) / (4.0*q[0]);
q[3] = (ex[1] - ey[0]) / (4.0*q[0]);
} else if (q1sq >= 0.25) {
q[1] = sqrt(q1sq);
q[0] = (a[2][1] - a[1][2]) / (4.0*q[1]);
q[2] = (a[0][1] + a[1][0]) / (4.0*q[1]);
q[3] = (a[2][0] + a[0][2]) / (4.0*q[1]);
q[0] = (ey[2] - ez[1]) / (4.0*q[1]);
q[2] = (ey[0] + ex[1]) / (4.0*q[1]);
q[3] = (ex[2] + ez[0]) / (4.0*q[1]);
} else if (q2sq >= 0.25) {
q[2] = sqrt(q2sq);
q[0] = (a[0][2] - a[2][0]) / (4.0*q[2]);
q[1] = (a[0][1] + a[1][0]) / (4.0*q[2]);
q[2] = (a[1][2] + a[2][1]) / (4.0*q[2]);
q[0] = (ez[0] - ex[2]) / (4.0*q[2]);
q[1] = (ey[0] + ex[1]) / (4.0*q[2]);
q[3] = (ez[1] + ey[2]) / (4.0*q[2]);
} else if (q3sq >= 0.25) {
q[3] = sqrt(q3sq);
q[0] = (a[1][0] - a[0][1]) / (4.0*q[3]);
q[1] = (a[0][2] + a[2][0]) / (4.0*q[3]);
q[2] = (a[1][2] + a[2][1]) / (4.0*q[3]);
q[0] = (ex[1] - ey[0]) / (4.0*q[3]);
q[1] = (ez[0] + ex[2]) / (4.0*q[3]);
q[2] = (ez[1] + ey[2]) / (4.0*q[3]);
} else
error->all("Quaternion creation numeric error");
normalize(q);
}
/* ----------------------------------------------------------------------
compute space-frame ex,ey,ez from current quaternion q
ex,ey,ez = space-frame coords of 1st,2nd,3rd principal axis
operation is ex = q' d q = Q d, where d is (1,0,0) = 1st axis in body frame
------------------------------------------------------------------------- */
void FixRigid::exyz_from_q(double *q, double *ex, double *ey, double *ez)
{
ex[0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
ex[1] = 2.0 * (q[1]*q[2] + q[0]*q[3]);
ex[2] = 2.0 * (q[1]*q[3] - q[0]*q[2]);
ey[0] = 2.0 * (q[1]*q[2] - q[0]*q[3]);
ey[1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
ey[2] = 2.0 * (q[2]*q[3] + q[0]*q[1]);
ez[0] = 2.0 * (q[1]*q[3] + q[0]*q[2]);
ez[1] = 2.0 * (q[2]*q[3] - q[0]*q[1]);
ez[2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
}
/* ----------------------------------------------------------------------
quaternion multiply: c = a*b where a = (0,a)
------------------------------------------------------------------------- */
@ -1204,27 +1226,6 @@ void FixRigid::omega_from_mq(double *m, double *ex, double *ey, double *ez,
w[2] = wbody[0]*ex[2] + wbody[1]*ey[2] + wbody[2]*ez[2];
}
/* ----------------------------------------------------------------------
compute space-frame ex,ey,ez from current quaternion q
ex,ey,ez = space-frame coords of 1st,2nd,3rd principal axis
operation is ex = q' d q = Q d, where d is (1,0,0) = 1st axis in body frame
------------------------------------------------------------------------- */
void FixRigid::exyz_from_q(double *q, double *ex, double *ey, double *ez)
{
ex[0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
ex[1] = 2.0 * (q[1]*q[2] + q[0]*q[3]);
ex[2] = 2.0 * (q[1]*q[3] - q[0]*q[2]);
ey[0] = 2.0 * (q[1]*q[2] - q[0]*q[3]);
ey[1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
ey[2] = 2.0 * (q[2]*q[3] + q[0]*q[1]);
ez[0] = 2.0 * (q[1]*q[3] + q[0]*q[2]);
ez[1] = 2.0 * (q[2]*q[3] - q[0]*q[1]);
ez[2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
}
/* ----------------------------------------------------------------------
set space-frame coords and velocity of each atom in each rigid body
x = Q displace + Xcm, mapped back to periodic box

4
src/fix_rigid.h
View File

@ -68,14 +68,14 @@ class FixRigid : public Fix {
int jacobi(double **, double *, double **);
void rotate(double **, int, int, int, int, double, double);
void qcreate(double **, double *);
void q_from_exyz(double *, double *, double *, double *);
void exyz_from_q(double *, double *, double *, double *);
void multiply(double *, double *, double *);
void normalize(double *);
void richardson(double *, double *, double *, double *,
double *, double *, double *);
void omega_from_mq(double *, double *, double *,
double *, double *, double *);
void exyz_from_q(double *, double *, double *, double *);
void set_xv();
void set_v();
};