void bond_xtal_origin_update (int iw)
{
register int i,j;
int k;
double *new_s, ds[3], tmp[3];
if (temporary_disable_bond) return;
MALLOC( bond_xtal_origin_update, new_s, DIMENSION*np, double );
V3mM3 (n[iw].xtal_origin, HI, ds);
V3TRIM (ds, ds);
for (i=0; i<np; i++)
{
V3SUB ( &(s[DIMENSION*i]), ds, &(new_s[DIMENSION*i]) );
V3TriM ( &(new_s[DIMENSION*i]) );
}
if (n[iw].bond_mode == BOND_MODE_USER)
for (k=0; k<C->n_cylinders; k++)
{
i = CylinderAtoms[2*k];
j = CylinderAtoms[2*k+1];
V3SUB (&(new_s[DIMENSION*j]), &(new_s[DIMENSION*i]), tmp);
if ( V3NEED_IMAGE(tmp) )
{ /* g<0 means geometric invisibility */
C->CYLINDER[k].g = -fabs(C->CYLINDER[k].g);
C->CYLINDER[k].radius = -fabs(C->CYLINDER[k].radius);
}
else
{
C->CYLINDER[k].g = fabs(C->CYLINDER[k].g);
C->CYLINDER[k].radius = fabs(C->CYLINDER[k].radius);
V3EQV (B->BALL[i].x, C->CYLINDER[k].x0);
}
}
else
for (i=0; i<np; i++)
for (j=N->idx[i]; j<N->idx[i+1]; j++)
{
V3SUB (&(new_s[DIMENSION*N->list[j]]),
&(new_s[DIMENSION*i]), tmp);
if ( V3NEED_IMAGE(tmp) )
{ /* g<0 means geometric invisibility */
C->CYLINDER[j].g = -fabs(C->CYLINDER[j].g);
C->CYLINDER[j].radius = -fabs(C->CYLINDER[j].radius);
}
else
{
C->CYLINDER[j].g = BOND_G(i, N->list[j]);
V3EQV (B->BALL[i].x, C->CYLINDER[j].x0);
if (C->CYLINDER[j].r >= 0)
C->CYLINDER[j].radius = n[iw].bond_radius;
}
}
free (new_s);
n[iw].bond_xtal_origin_need_update = FALSE;
return;
} /* end bond_xtal_origin_update() */
/* Allocate bonds */
void Config_to_3D_Bonds (double bond_radius)
{
register int i,j;
AX_Float ds[3], DS[3];
AX_3D_Cylinders_Realloc (C, N->idx[np]);
for (i=0; i<np; i++)
for (j=N->idx[i]; j<N->idx[i+1]; j++)
{
V3EQV ( B->BALL[i].x, C->CYLINDER[j].x0 );
V3SUB ( &s[DIMENSION*N->list[j]], &s[DIMENSION*i], ds );
V3IMAGE ( ds, DS );
V3mM3 ( DS, H, C->CYLINDER[j].axis );
AX_V3NORMALIZE ( C->CYLINDER[j].axis, C->CYLINDER[j].axis[3] );
BONDCOLOR (i, N->list[j], j);
if (V3NEED_IMAGE(ds))
{
C->CYLINDER[j].g = -1;
C->CYLINDER[j].radius = -1;
}
else C->CYLINDER[j].radius = bond_radius;
}
return;
} /* end Config_to_3D_Bonds() */
