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merge in current develop

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This commit is contained in:
Steve Plimpton
2022-03-11 10:01:25 -07:00
parent 8ba4e7e897 9b989b1860
commit 1a04eabb5e
3529 changed files with 108434 additions and 51454 deletions
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71
src/comm.cpp
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@ -201,8 +201,9 @@ void Comm::init()
if (ghost_velocity) size_forward += atom->avec->size_velocity;
if (ghost_velocity) size_border += atom->avec->size_velocity;
for (int i = 0; i < modify->nfix; i++)
size_border += modify->fix[i]->comm_border;
const auto &fix_list = modify->get_fix_list();
for (const auto &fix : fix_list)
size_border += fix->comm_border;
// per-atom limits for communication
// maxexchange = max # of datums in exchange comm, set in exchange()
@ -217,9 +218,9 @@ void Comm::init()
if (force->pair) maxforward = MAX(maxforward,force->pair->comm_forward);
if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse);
for (int i = 0; i < modify->nfix; i++) {
maxforward = MAX(maxforward,modify->fix[i]->comm_forward);
maxreverse = MAX(maxreverse,modify->fix[i]->comm_reverse);
for (const auto &fix : fix_list) {
maxforward = MAX(maxforward,fix->comm_forward);
maxreverse = MAX(maxreverse,fix->comm_reverse);
}
for (int i = 0; i < modify->ncompute; i++) {
@ -241,12 +242,9 @@ void Comm::init()
maxexchange_atom = atom->avec->maxexchange;
int nfix = modify->nfix;
Fix **fix = modify->fix;
maxexchange_fix_dynamic = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
for (const auto &fix : fix_list)
if (fix->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI))
error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists");
@ -267,12 +265,9 @@ void Comm::init()
void Comm::init_exchange()
{
int nfix = modify->nfix;
Fix **fix = modify->fix;
maxexchange_fix = 0;
for (int i = 0; i < nfix; i++)
maxexchange_fix += fix[i]->maxexchange;
for (const auto &fix : modify->get_fix_list())
maxexchange_fix += fix->maxexchange;
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
@ -395,9 +390,7 @@ void Comm::modify_params(int narg, char **arg)
iarg += 1;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1;
else if (strcmp(arg[iarg+1],"no") == 0) ghost_velocity = 0;
else error->all(FLERR,"Illegal comm_modify command");
ghost_velocity = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal comm_modify command");
}
@ -783,13 +776,13 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
} else if (layout == Comm::LAYOUT_NONUNIFORM) {
if (triclinic == 0) {
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);
igx = utils::binary_search((x[0]-boxlo[0])/prd[0],procgrid[0],xsplit);
igy = utils::binary_search((x[1]-boxlo[1])/prd[1],procgrid[1],ysplit);
igz = utils::binary_search((x[2]-boxlo[2])/prd[2],procgrid[2],zsplit);
} else {
igx = binary(x[0],procgrid[0],xsplit);
igy = binary(x[1],procgrid[1],ysplit);
igz = binary(x[2],procgrid[2],zsplit);
igx = utils::binary_search(x[0],procgrid[0],xsplit);
igy = utils::binary_search(x[1],procgrid[1],ysplit);
igz = utils::binary_search(x[2],procgrid[2],zsplit);
}
}
@ -803,36 +796,6 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
return grid2proc[igx][igy][igz];
}
/* ----------------------------------------------------------------------
binary search for value in N-length ascending vec
value may be outside range of vec limits
always return index from 0 to N-1 inclusive
return 0 if value < vec[0]
reutrn N-1 if value >= vec[N-1]
return index = 1 to N-2 if vec[index] <= value < vec[index+1]
------------------------------------------------------------------------- */
int Comm::binary(double value, int n, double *vec)
{
int lo = 0;
int hi = n-1;
if (value < vec[lo]) return lo;
if (value >= vec[hi]) return hi;
// insure vec[lo] <= value < vec[hi] at every iteration
// done when lo,hi are adjacent
int index = (lo+hi)/2;
while (lo < hi-1) {
if (value < vec[index]) hi = index;
else if (value >= vec[index]) lo = index;
index = (lo+hi)/2;
}
return index;
}
/* ----------------------------------------------------------------------
partition a global regular grid into one brick-shaped sub-grid per proc
if grid point is inside my sub-domain I own it,