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@8365 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-06-21 16:27:12 +00:00
parent 7398f3eca3
commit 31bc11ee34
9 changed files with 616 additions and 114 deletions
Download Patch File Download Diff File Expand all files Collapse all files

131
src/irregular.cpp
View File

@ -117,13 +117,14 @@ void Irregular::migrate_atoms()
int nsendatom = 0;
int *sizes = new int[nlocal];
int *proclist = new int[nlocal];
int igx,igy,igz;
int i = 0;
while (i < nlocal) {
if (x[i][0] < sublo[0] || x[i][0] >= subhi[0] ||
x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
proclist[nsendatom] = coord2proc(x[i]);
proclist[nsendatom] = coord2proc(x[i],igx,igy,igz);
if (proclist[nsendatom] != me) {
if (nsend > maxsend) grow_send(nsend,1);
sizes[nsendatom] = avec->pack_exchange(i,&buf_send[nsend]);
@ -157,6 +158,90 @@ void Irregular::migrate_atoms()
if (map_style) atom->map_set();
}
/* ----------------------------------------------------------------------
check if any atoms need to migrate further than one proc away in any dim
if not, caller can decide to use comm->exchange() instead
atoms must be remapped to be inside simulation box before this is called
for triclinic: atoms must be in lamda coords (0-1) before this is called
return 1 if migrate required, 0 if not
------------------------------------------------------------------------- */
int Irregular::migrate_check()
{
return 1;
// subbox bounds for orthogonal or triclinic box
// other comm/domain data used by coord2proc()
double *sublo,*subhi;
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
uniform = comm->uniform;
xsplit = comm->xsplit;
ysplit = comm->ysplit;
zsplit = comm->zsplit;
boxlo = domain->boxlo;
prd = domain->prd;
// loop over atoms, check for any that are not in my sub-box
// assign which proc it belongs to via coord2proc()
// if logical igx,igy,igz of newproc > one away from myloc, set flag = 1
// this check needs to observe PBC
// cannot check via comm->procneigh since it ignores PBC
AtomVec *avec = atom->avec;
double **x = atom->x;
int nlocal = atom->nlocal;
int *periodicity = domain->periodicity;
int *myloc = comm->myloc;
int *procgrid = comm->procgrid;
int newproc,igx,igy,igz,glo,ghi;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (x[i][0] < sublo[0] || x[i][0] >= subhi[0] ||
x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
newproc = coord2proc(x[i],igx,igy,igz);
glo = myloc[0] - 1;
ghi = myloc[0] + 1;
if (periodicity[0]) {
if (glo < 0) glo = procgrid[0] - 1;
if (ghi >= procgrid[0]) ghi = 0;
}
if (igx != myloc[0] && igx != glo && igx != ghi) flag = 1;
glo = myloc[1] - 1;
ghi = myloc[1] + 1;
if (periodicity[1]) {
if (glo < 0) glo = procgrid[1] - 1;
if (ghi >= procgrid[1]) ghi = 0;
}
if (igx != myloc[1] && igx != glo && igx != ghi) flag = 1;
glo = myloc[2] - 1;
ghi = myloc[2] + 1;
if (periodicity[2]) {
if (glo < 0) glo = procgrid[2] - 1;
if (ghi >= procgrid[2]) ghi = 0;
}
if (igx != myloc[2] && igx != glo && igx != ghi) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
return flagall;
}
/* ----------------------------------------------------------------------
create a communication plan for atoms
n = # of atoms to send
@ -613,43 +698,43 @@ void Irregular::destroy_data()
x will be in box (orthogonal) or lamda coords (triclinic)
for uniform = 1, directly calculate owning proc
for non-uniform, iteratively find owning proc via binary search
return owning proc ID via grid2proc
return igx,igy,igz = logical grid loc of owing proc within 3d grid of procs
------------------------------------------------------------------------- */
int Irregular::coord2proc(double *x)
int Irregular::coord2proc(double *x, int &igx, int &igy, int &igz)
{
int loc[3];
if (uniform) {
if (triclinic == 0) {
loc[0] = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
loc[1] = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
loc[2] = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
igx = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
igy = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
igz = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
} else {
loc[0] = static_cast<int> (procgrid[0] * x[0]);
loc[1] = static_cast<int> (procgrid[1] * x[1]);
loc[2] = static_cast<int> (procgrid[2] * x[2]);
igx = static_cast<int> (procgrid[0] * x[0]);
igy = static_cast<int> (procgrid[1] * x[1]);
igz = static_cast<int> (procgrid[2] * x[2]);
}
} else {
if (triclinic == 0) {
loc[0] = binary((x[0]-boxlo[0])/prd[0],procgrid[0],xsplit);
loc[1] = binary((x[1]-boxlo[1])/prd[1],procgrid[1],ysplit);
loc[2] = binary((x[2]-boxlo[2])/prd[2],procgrid[2],zsplit);
igx = binary((x[0]-boxlo[0])/prd[0],procgrid[0],xsplit);
igy = binary((x[1]-boxlo[1])/prd[1],procgrid[1],ysplit);
igz = binary((x[2]-boxlo[2])/prd[2],procgrid[2],zsplit);
} else {
loc[0] = binary(x[0],procgrid[0],xsplit);
loc[1] = binary(x[1],procgrid[1],ysplit);
loc[2] = binary(x[2],procgrid[2],zsplit);
igx = binary(x[0],procgrid[0],xsplit);
igy = binary(x[1],procgrid[1],ysplit);
igz = binary(x[2],procgrid[2],zsplit);
}
}
if (loc[0] < 0) loc[0] = 0;
if (loc[0] >= procgrid[0]) loc[0] = procgrid[0] - 1;
if (loc[1] < 0) loc[1] = 0;
if (loc[1] >= procgrid[1]) loc[1] = procgrid[1] - 1;
if (loc[2] < 0) loc[2] = 0;
if (loc[2] >= procgrid[2]) loc[2] = procgrid[2] - 1;
if (igx < 0) igx = 0;
if (igx >= procgrid[0]) igx = procgrid[0] - 1;
if (igy < 0) igy = 0;
if (igy >= procgrid[1]) igy = procgrid[1] - 1;
if (igz < 0) igz = 0;
if (igz >= procgrid[2]) igz = procgrid[2] - 1;
return grid2proc[loc[0]][loc[1]][loc[2]];
return grid2proc[igx][igy][igz];
}
/* ----------------------------------------------------------------------