output of fix ave/grid
This commit is contained in:
Steve Plimpton
@ -169,6 +169,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// optional args
|
||||
|
||||
/*
|
||||
normflag = ALL;
|
||||
scaleflag = ATOM;
|
||||
ave = ONE;
|
||||
@ -204,6 +205,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
} else error->all(FLERR,"Illegal fix ave/grid command");
|
||||
}
|
||||
*/
|
||||
|
||||
// if wildcard expansion occurred, free earg memory from exapnd_args()
|
||||
|
||||
@ -449,7 +451,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
|
||||
"ave/grid:vec3d");
|
||||
}
|
||||
|
||||
// zero the grid since dump may access it on timestep 0
|
||||
// zero the grid and counts since dump may access it on timestep 0
|
||||
|
||||
zero_grid();
|
||||
|
||||
@ -607,25 +609,11 @@ void FixAveGrid::end_of_step()
|
||||
if (ntimestep != nvalid) return;
|
||||
nvalid_last = nvalid;
|
||||
|
||||
// zero owned and ghost grid points if first step
|
||||
// zero atom count per bin for ATOM mode
|
||||
// NOTE: when should counts be zeroed
|
||||
// NOTE: is anything normalized by count ?
|
||||
// NOTE: can count be output ?
|
||||
// zero owned and ghost grid points and counts if first sample in epoch
|
||||
|
||||
if (irepeat == 0) zero_grid();
|
||||
|
||||
if (modeatom) {
|
||||
if (dimension == 2) {
|
||||
if (ngridout) memset(&count2d[nylo_out][nxlo_out],0,
|
||||
ngridout*sizeof(double));
|
||||
} else {
|
||||
if (ngridout) memset(&count3d[nzlo_out][nylo_out][nxlo_out],0,
|
||||
ngridout*sizeof(double));
|
||||
}
|
||||
}
|
||||
|
||||
// set local per-grid values for either ATOM or GRID mode
|
||||
// accumulate per-grid values for one sample for either ATOM or GRID mode
|
||||
// per-atom compute/fix/variable may invoke computes so wrap with clear/add
|
||||
|
||||
if (modeatom) {
|
||||
@ -649,15 +637,15 @@ void FixAveGrid::end_of_step()
|
||||
nvalid = ntimestep+pergrid_freq - ((bigint) nrepeat-1)*nevery;
|
||||
if (modeatom) modify->addstep_compute(nvalid);
|
||||
|
||||
// ghost to owned grid communication for atom mode
|
||||
// NOTE: still need to implement pack/unpack methods, for count as well?
|
||||
// for ATOM mode, perform ghost to owned grid communication
|
||||
// nvalues + 1 more for atom count
|
||||
|
||||
if (modeatom) {
|
||||
if (dimension == 2)
|
||||
grid2d->reverse_comm(Grid2d::FIX,this,1,sizeof(double),0,
|
||||
grid2d->reverse_comm(Grid2d::FIX,this,nvalues+1,sizeof(double),0,
|
||||
grid_buf1,grid_buf2,MPI_DOUBLE);
|
||||
else
|
||||
grid3d->reverse_comm(Grid3d::FIX,this,1,sizeof(double),0,
|
||||
grid3d->reverse_comm(Grid3d::FIX,this,nvalues+1,sizeof(double),0,
|
||||
grid_buf1,grid_buf2,MPI_DOUBLE);
|
||||
}
|
||||
|
||||
@ -665,47 +653,91 @@ void FixAveGrid::end_of_step()
|
||||
|
||||
if (ngridout == 0) return;
|
||||
|
||||
// average the final result for the Nfreq timestep
|
||||
// just loop over owned grid points
|
||||
|
||||
double invrepeat = 1.0/nrepeat;
|
||||
// average the final results for the Nfreq output
|
||||
// for ATOM mode, divide total values by total count
|
||||
// for GRID mode, divide total values by # of samples
|
||||
|
||||
if (dimension == 2) {
|
||||
if (nvalues == 1) {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
vec2d[iy][ix] *= invrepeat;
|
||||
if (modeatom) {
|
||||
double count,invcount;
|
||||
|
||||
if (dimension == 2) {
|
||||
if (nvalues == 1) {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
count = count2d[iy][ix];
|
||||
if (count) {
|
||||
vec2d[iy][ix] /= count;
|
||||
count2d[iy][iz] /= nrepeat;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
count = count2d[iy][ix];
|
||||
if (count) {
|
||||
invcount = 1.0/count;
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array2d[iy][ix][m] *= invcount;
|
||||
count2d[iy][iz] /= nrepeat;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array2d[iy][ix][m] *= invrepeat;
|
||||
}
|
||||
} else {
|
||||
if (nvalues == 1) {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
vec3d[iz][iy][ix] *= invrepeat;
|
||||
} else {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array3d[iz][iy][ix][m] *= invrepeat;
|
||||
if (nvalues == 1) {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
count = count3d[iz][iy][ix];
|
||||
if (count) {
|
||||
vec3d[iz][iy][ix] /= count;
|
||||
count3d[iz][iy][iz] /= nrepeat;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
count = count3d[iz][iy][ix];
|
||||
if (count) {
|
||||
invcount = 1.0/count;
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array3d[iz][iy][ix][m] *= invcount;
|
||||
count3d[iz][iy][iz] /= nrepeat;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
subset of grid assigned to each proc may have changed
|
||||
called by load balancer when proc subdomains are adjusted
|
||||
not supported for now, b/c requires per-grid values to persist, i.e. a remap()
|
||||
------------------------------------------------------------------------- */
|
||||
if (modegrid) {
|
||||
double invrepeat = 1.0/nrepeat;
|
||||
|
||||
void FixAveGrid::reset_grid()
|
||||
{
|
||||
error->all(FLERR,"Fix ave/grid does not support load balancing (yet)");
|
||||
if (dimension == 2) {
|
||||
if (nvalues == 1) {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
vec2d[iy][ix] *= invrepeat;
|
||||
} else {
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array2d[iy][ix][m] *= invrepeat;
|
||||
}
|
||||
} else {
|
||||
if (nvalues == 1) {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
vec3d[iz][iy][ix] *= invrepeat;
|
||||
} else {
|
||||
for (iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (ix = nxlo_in; ix <= nxhi_in; ix++)
|
||||
for (m = 0; m <= nvalues; m++)
|
||||
array3d[iz][iy][ix][m] *= invrepeat;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1021,29 +1053,119 @@ void FixAveGrid::grid2grid()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
zero grid values incluing ghost cells
|
||||
if ATOM mode, also zero per-cell counts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveGrid::zero_grid()
|
||||
{
|
||||
if (!ngridout) return;
|
||||
|
||||
if (dimension == 2) {
|
||||
if (nvalues == 1) {
|
||||
if (ngridout) memset(&vec2d[nylo_out][nxlo_out],0,
|
||||
ngridout*sizeof(double));
|
||||
} else {
|
||||
if (ngridout) memset(&array2d[nylo_out][nxlo_out][0],0,
|
||||
ngridout*nvalues*sizeof(double));
|
||||
if (nvalues == 1)
|
||||
memset(&vec2d[nylo_out][nxlo_out],0, ngridout*sizeof(double));
|
||||
else
|
||||
memset(&array2d[nylo_out][nxlo_out][0],0,ngridout*nvalues*sizeof(double));
|
||||
if (modeatom)
|
||||
memset(&count2d[nylo_out][nxlo_out],0,ngridout*sizeof(double));
|
||||
} else {
|
||||
if (nvalues == 1)
|
||||
memset(&vec3d[nzlo_out][nylo_out][nxlo_out],0,ngridout*sizeof(double));
|
||||
else
|
||||
memset(&array3d[nzlo_out][nylo_out][nxlo_out][0],0,
|
||||
ngridout*nvalues*sizeof(double));
|
||||
if (modeatom)
|
||||
memset(&count3d[nzlo_out][nylo_out][nxlo_out],0,ngridout*sizeof(double));
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack ghost values into buf to send to another proc
|
||||
nvalues per grid point + count
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveGrid::pack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *list)
|
||||
{
|
||||
int i,j,m;
|
||||
|
||||
auto buf = (double *) vbuf;
|
||||
double *count,*data,*values;
|
||||
m = 0;
|
||||
|
||||
if (dimension == 2) {
|
||||
count = &count2d[nylo_out][nxlo_out];
|
||||
if (nvalues == 1) data = &vec2d[nylo_out][nxlo_out];
|
||||
else data = &array2d[nylo_out][nxlo_out][0];
|
||||
} else if (dimension == 3) {
|
||||
count = &count3d[nzlo_out][nylo_out][nxlo_out];
|
||||
if (nvalues == 1) data = &vec3d[nzlo_out][nylo_out][nxlo_out];
|
||||
else data = &array3d[nzlo_out][nylo_out][nxlo_out][0];
|
||||
}
|
||||
|
||||
if (nvalues == 1) {
|
||||
for (i = 0; i < nlist; i++) {
|
||||
buf[m++] = count[list[i]];
|
||||
buf[m++] = data[list[i]];
|
||||
}
|
||||
} else {
|
||||
if (nvalues == 1) {
|
||||
if (ngridout) memset(&vec3d[nzlo_out][nylo_out][nxlo_out],0,
|
||||
ngridout*sizeof(double));
|
||||
} else {
|
||||
if (ngridout) memset(&array3d[nzlo_out][nylo_out][nxlo_out][0],0,
|
||||
ngridout*nvalues*sizeof(double));
|
||||
for (i = 0; i < nlist; i++) {
|
||||
buf[m++] = count[list[i]];
|
||||
values = &data[nvalues*list[i]];
|
||||
for (j = 0; j <= nvalues; j++)
|
||||
buf[m++] = values[j];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack another proc's ghost values from buf and add to own values
|
||||
nvalues per grid point + count
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveGrid::unpack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *list)
|
||||
{
|
||||
int i,j,m;
|
||||
|
||||
auto buf = (double *) vbuf;
|
||||
double *count,*data,*values;
|
||||
m = 0;
|
||||
|
||||
if (dimension == 2) {
|
||||
count = &count2d[nylo_out][nxlo_out];
|
||||
if (nvalues == 1) data = &vec2d[nylo_out][nxlo_out];
|
||||
else data = &array2d[nylo_out][nxlo_out][0];
|
||||
} else if (dimension == 3) {
|
||||
count = &count3d[nzlo_out][nylo_out][nxlo_out];
|
||||
if (nvalues == 1) data = &vec3d[nzlo_out][nylo_out][nxlo_out];
|
||||
else data = &array3d[nzlo_out][nylo_out][nxlo_out][0];
|
||||
}
|
||||
|
||||
if (nvalues == 1) {
|
||||
for (i = 0; i < nlist; i++) {
|
||||
count[list[i]] += buf[m++];
|
||||
data[list[i]] += buf[m++];
|
||||
}
|
||||
} else {
|
||||
for (i = 0; i < nlist; i++) {
|
||||
count[list[i]] = buf[m++];
|
||||
values = &data[nvalues*list[i]];
|
||||
for (j = 0; j <= nvalues; j++)
|
||||
values[j] = buf[m++];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
subset of grid assigned to each proc may have changed
|
||||
called by load balancer when proc subdomains are adjusted
|
||||
not supported for now, b/c requires per-grid values to persist, i.e. a remap()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveGrid::reset_grid()
|
||||
{
|
||||
error->all(FLERR,"Fix ave/grid does not support load balancing (yet)");
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return index of grid associated with name
|
||||
this class can store M named grids, indexed 0 to M-1
|
||||
@ -1094,7 +1216,10 @@ int FixAveGrid::get_griddata_by_name(int igrid, char *name, int &ncol)
|
||||
else ncol = nvalues;
|
||||
return 0;
|
||||
}
|
||||
if (igrid == 0 && strcmp(name,"count") == 0) {
|
||||
|
||||
// count is only produced for ATOM mode
|
||||
|
||||
if (modeatom && igrid == 0 && strcmp(name,"count") == 0) {
|
||||
ncol = 0;
|
||||
return 1;
|
||||
}
|
||||
@ -1129,12 +1254,12 @@ void *FixAveGrid::get_griddata_by_index(int index)
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
NOTE: add more memory tallying
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixAveGrid::memory_usage()
|
||||
{
|
||||
double bytes = (double) ngridout * nvalues * sizeof(double);
|
||||
double bytes = (double) ngridout * nvalues * sizeof(double); // vec/array 2d/3d
|
||||
if (modeatom) bytes += (double) ngridout * sizeof(double); // count2d/3d
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user