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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8391 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-25 16:42:20 +00:00
parent bee842bed7
commit e8ff810ee7
78 changed files with 396 additions and 474 deletions
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47
src/domain.cpp
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@ -580,19 +580,6 @@ void Domain::box_too_small_check()
"Bond/angle/dihedral extent > half of periodic box length");
}
/* ----------------------------------------------------------------------
minimum image convention check
return 1 if any distance > 1/2 of box size
------------------------------------------------------------------------- */
int Domain::minimum_image_check(double dx, double dy, double dz)
{
if (xperiodic && fabs(dx) > xprd_half) return 1;
if (yperiodic && fabs(dy) > yprd_half) return 1;
if (zperiodic && fabs(dz) > zprd_half) return 1;
return 0;
}
/* ----------------------------------------------------------------------
minimum image convention
use 1/2 of box size as test
@ -717,6 +704,40 @@ void Domain::minimum_image(double *delta)
}
}
/* ----------------------------------------------------------------------
return local index of atom J or any of its images that is closest to atom I
if J is not a valid index like -1, just return it
------------------------------------------------------------------------- */
int Domain::closest_image(int i, int j)
{
if (j < 0) return j;
int *sametag = atom->sametag;
double **x = atom->x;
double *xi = x[i];
int closest = j;
double delx = xi[0] - x[j][0];
double dely = xi[1] - x[j][1];
double delz = xi[2] - x[j][2];
double rsqmin = delx*delx + dely*dely + delz*delz;
double rsq;
while (sametag[j] >= 0) {
j = sametag[j];
delx = xi[0] - x[j][0];
dely = xi[1] - x[j][1];
delz = xi[2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = j;
}
}
return closest;
}
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed