ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8312 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-06-18 23:49:36 +00:00
parent 5208299da4
commit bb48c5ccdc
5 changed files with 24 additions and 16 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
src/domain.cpp
View File

@ -98,12 +98,6 @@ Domain::~Domain()
void Domain::init()
{
// check for too small a periodic box for molecular system
if (atom->molecular && box_too_small())
error->all(FLERR,"Bond/angle/dihedral extent must be < "
"half of periodic box dimension");
// set box_change if box dimensions/shape ever changes
// due to shrink-wrapping, fixes that change volume (npt, vol/rescale, etc)
@ -525,16 +519,16 @@ void Domain::pbc()
/* ----------------------------------------------------------------------
check that no pair of atoms in a bonded interaction
are further apart than half a periodic box length
return 1 if any pair is, else 0
------------------------------------------------------------------------- */
int Domain::box_too_small()
void Domain::box_too_small_check()
{
int i,j,k;
// only need to check if some dimension is periodic
// only need to check if system is molecluar and some dimension is periodic
if (!xperiodic && !yperiodic && (dimension == 2 || !zperiodic)) return 0;
if (!atom->molecular) return;
if (!xperiodic && !yperiodic && (dimension == 2 || !zperiodic)) return;
// maxbondall = longest current bond length
// NOTE: if box is tiny (less than 2 * bond-length),
@ -552,7 +546,7 @@ int Domain::box_too_small()
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
k = atom->map(bond_atom[i][j]);
if (k < 0) error->one(FLERR,"Bond atom missing in box size check");
if (k == -1) error->one(FLERR,"Bond atom missing in box size check");
delx = x[i][0] - x[k][0];
dely = x[i][1] - x[k][1];
delz = x[i][2] - x[k][2];
@ -576,10 +570,14 @@ int Domain::box_too_small()
// else when use minimg() in bond/angle/dihdral compute,
// could calculate incorrect distance between 2 atoms
if (xperiodic && maxdelta > xprd_half) return 1;
if (yperiodic && maxdelta > yprd_half) return 1;
if (dimension == 3 && zperiodic && maxdelta > zprd_half) return 1;
return 0;
int flag = 0;
if (xperiodic && maxdelta > xprd_half) flag = 1;
if (yperiodic && maxdelta > yprd_half) flag = 1;
if (dimension == 3 && zperiodic && maxdelta > zprd_half) flag = 1;
if (flag)
error->all(FLERR,
"Bond/angle/dihedral extent > half of periodic box length");
}
/* ----------------------------------------------------------------------