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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@706 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-06-29 17:11:02 +00:00
parent 33d2806fd8
commit 884cf474f1
2 changed files with 20 additions and 13 deletions
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29
src/create_atoms.cpp
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@ -260,9 +260,16 @@ void CreateAtoms::add_many()
if (zmin < 0.0) klo--;
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// on lower boundary, allows triclinic atoms just outside box to be added
// on upper boundary, prevents atoms with lower images from being added
// if periodic:
// should create exactly 1 atom when 2 images are both "on" the boundary
// either image may be slightly inside/outside true box due to round-off
// if I am lo proc, decrement lower bound by EPSILON
// this will insure lo image is created
// if I am hi proc, decrement upper bound by 2.0*EPSILON
// this will insure hi image is not created
// thus insertion box is EPSILON smaller than true box
// and is shifted away from true boundary
// which is where atoms are likely to be generated
double sublo[3],subhi[3];
@ -277,20 +284,20 @@ void CreateAtoms::add_many()
}
if (domain->xperiodic) {
if (triclinic && comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= EPSILON;
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*EPSILON;
}
if (domain->yperiodic) {
if (triclinic && comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= EPSILON;
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*EPSILON;
}
if (domain->zperiodic) {
if (triclinic && comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= EPSILON;
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*EPSILON;
}
// iterate on 3d periodic lattice using loop bounds
// invoke add_atom for nbasis atoms in each unit cell
// iterate on 3d periodic lattice of unit cells using loop bounds
// iterate on nbasis atoms in each unit cell
// convert lattice coords to box coords
// add atom if it meets all criteria

4
src/lammps.cpp
View File

@ -307,7 +307,7 @@ void LAMMPS::init()
// used by fix shear_history::unpack_restart()
// when force->pair->gran_history creates fix ??
modify->init(); // modify must come after update, force, atom
neighbor->init(); // neighbor must come after force, modify (due to min)
neighbor->init(); // neighbor must come after force, modify
output->init(); // output must come after domain, force, modify
comm->init(); // comm must come after force, modify
timer->init();
@ -329,7 +329,7 @@ void LAMMPS::destroy()
delete output;
delete modify; // modify must come after output, force, update
// since they delete fixes
delete atom; // must come after modify, neighbor
delete atom; // atom must come after modify, neighbor
// since fixes delete callbacks in atom
delete timer;
}