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debug of fix ave/grid

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This commit is contained in:
Steve Plimpton
2022-08-23 09:58:58 -06:00
parent 37e9bf54ab
commit b6583eb681
4 changed files with 193 additions and 23 deletions
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188
src/fix_ave_grid.cpp
View File

@ -407,7 +407,12 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
nxlo_in, nxhi_in, nylo_in, nyhi_in,
nxlo_out, nxhi_out, nylo_out, nyhi_out);
// ngrid_buf12 converted to nvalues + count
grid2d->setup(ngrid_buf1, ngrid_buf2);
ngrid_buf1 *= nvalues + 1;
ngrid_buf2 *= nvalues + 1;
memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1");
memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2");
@ -419,7 +424,12 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
nxlo_out, nxhi_out, nylo_out, nyhi_out,
nzlo_out, nzhi_out);
// ngrid_buf12 converted to nvalues + count
grid3d->setup(ngrid_buf1, ngrid_buf2);
ngrid_buf1 *= nvalues + 1;
ngrid_buf2 *= nvalues + 1;
memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1");
memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2");
@ -791,7 +801,7 @@ void FixAveGrid::atom2grid()
}
skip[i] = 0;
count2d[iy][ix] += 1.0;
count2d_sample[iy][ix] += 1.0;
bin[i][0] = iy;
bin[i][1] = ix;
}
@ -824,7 +834,7 @@ void FixAveGrid::atom2grid()
}
skip[i] = 0;
count3d[iz][iy][ix] += 1.0;
count3d_sample[iz][iy][ix] += 1.0;
bin[i][0] = iz;
bin[i][1] = iy;
bin[i][2] = ix;
@ -857,7 +867,7 @@ void FixAveGrid::atom2grid()
}
} else
for (i = 0; i < nlocal; i++) {
if (skip[i])
if (!skip[i])
array2d_sample[bin[i][0]][bin[i][1]][m] += attribute[i][j];
}
} else {
@ -897,7 +907,7 @@ void FixAveGrid::atom2grid()
}
} else
for (i = 0; i < nlocal; i++) {
if (skip[i]) {
if (!skip[i]) {
if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
else if (rmass) one = rmass[i];
else one = mass[type[i]];
@ -953,7 +963,7 @@ void FixAveGrid::atom2grid()
}
} else
for (i = 0; i < nlocal; i++) {
if (skip[i]) {
if (!skip[i]) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) one = rmass[i];
else one = mass[type[i]];
@ -1292,35 +1302,35 @@ void FixAveGrid::allocate_grid()
void FixAveGrid::deallocate_grid()
{
memory->destroy2d_offset(vec2d,nylo_out,nxlo_out);
memory->destroy2d_offset(array2d,nylo_out,nxlo_out);
memory->destroy3d_offset_last(array2d,nylo_out,nxlo_out);
memory->destroy2d_offset(count2d,nylo_out,nxlo_out);
memory->destroy2d_offset(vec2d_sample,nylo_out,nxlo_out);
memory->destroy2d_offset(array2d_sample,nylo_out,nxlo_out);
memory->destroy3d_offset_last(array2d_sample,nylo_out,nxlo_out);
memory->destroy2d_offset(count2d_sample,nylo_out,nxlo_out);
memory->destroy2d_offset(vec2d_epoch,nylo_out,nxlo_out);
memory->destroy2d_offset(array2d_epoch,nylo_out,nxlo_out);
memory->destroy3d_offset_last(array2d_epoch,nylo_out,nxlo_out);
memory->destroy2d_offset(count2d_epoch,nylo_out,nxlo_out);
memory->destroy2d_offset(vec2d_running,nylo_out,nxlo_out);
memory->destroy2d_offset(array2d_running,nylo_out,nxlo_out);
memory->destroy3d_offset_last(array2d_running,nylo_out,nxlo_out);
memory->destroy2d_offset(count2d_running,nylo_out,nxlo_out);
memory->destroy3d_offset(vec3d,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(array3d,nzlo_out,nylo_out,nxlo_out);
memory->destroy4d_offset_last(array3d,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(count3d,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vec3d_sample,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(array3d_sample,nzlo_out,nylo_out,nxlo_out);
memory->destroy4d_offset_last(array3d_sample,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(count3d_sample,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vec3d_epoch,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(array3d_epoch,nzlo_out,nylo_out,nxlo_out);
memory->destroy4d_offset_last(array3d_epoch,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(count3d_epoch,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vec3d_running,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(array3d_running,nzlo_out,nylo_out,nxlo_out);
memory->destroy4d_offset_last(array3d_running,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(count3d_running,nzlo_out,nylo_out,nxlo_out);
}
@ -1448,6 +1458,150 @@ void FixAveGrid::copy_epoch_to_sample()
}
}
/* ----------------------------------------------------------------------
copy sample grid values to output grid, just for owned grid cells
if ATOM mode, also copy per-cell counts
------------------------------------------------------------------------- */
void FixAveGrid::copy_sample_to_output()
{
int ix,iy,iz,m;
if (!ngridout) return;
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] = vec2d_sample[iy][ix];
} 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] = array2d_sample[iy][ix][m];
}
if (modeatom)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count2d[iy][ix] = count2d_sample[iy][ix];
} else {
if (nvalues == 1) {
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
vec3d[iz][iy][ix] = vec3d_sample[iz][iy][ix];
} else {
for (iz = nylo_in; iz <= nyhi_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] = array3d_sample[iz][iy][ix][m];
}
if (modeatom)
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count3d[iz][iy][ix] = count3d_sample[iz][iy][ix];
}
}
/* ----------------------------------------------------------------------
copy running grid values to output grid, just for owned grid cells
if ATOM mode, also copy per-cell counts
------------------------------------------------------------------------- */
void FixAveGrid::copy_running_to_output()
{
int ix,iy,iz,m;
if (!ngridout) return;
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] = vec2d_running[iy][ix];
} 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] = array2d_running[iy][ix][m];
}
if (modeatom)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count2d[iy][ix] = count2d_running[iy][ix];
} else {
if (nvalues == 1) {
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
vec3d[iz][iy][ix] = vec3d_running[iz][iy][ix];
} else {
for (iz = nylo_in; iz <= nyhi_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] = array3d_running[iz][iy][ix][m];
}
if (modeatom)
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count3d[iz][iy][ix] = count3d_running[iz][iy][ix];
}
}
/* ----------------------------------------------------------------------
sum sample grid values to running grid, just for owned grid cells
if ATOM mode, also copy per-cell counts
------------------------------------------------------------------------- */
void FixAveGrid::sum_sample_to_running()
{
int ix,iy,iz,m;
if (!ngridout) return;
if (dimension == 2) {
if (nvalues == 1) {
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
vec2d_running[iy][ix] += vec2d_sample[iy][ix];
} else {
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
for (m = 0; m <= nvalues; m++)
array2d_running[iy][ix][m] += array2d_sample[iy][ix][m];
}
if (modeatom)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count2d_running[iy][ix] += count2d_sample[iy][ix];
} else {
if (nvalues == 1) {
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
vec3d_running[iz][iy][ix] += vec3d_sample[iz][iy][ix];
} else {
for (iz = nylo_in; iz <= nyhi_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_running[iz][iy][ix][m] += array3d_sample[iz][iy][ix][m];
}
if (modeatom)
for (iz = nylo_in; iz <= nyhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
count3d_running[iz][iy][ix] += count3d_sample[iz][iy][ix];
}
}
/* ----------------------------------------------------------------------
normalize grid values and per-cell counts for ATOM mode for owned cells
numsamples = normalization factor
@ -1496,7 +1650,7 @@ void FixAveGrid::normalize_atom(int numsamples)
norm = mvv2e /((repeat*cdof + adof*count) * boltz);
else if (normflag == NONORM)
norm = 1.0/invrepeat;
else if (normflag == NONORM)
else
norm = 1.0/count;
vec2d_sample[iy][ix] *= norm;
count2d_sample[iy][ix] *= invrepeat;
@ -1507,7 +1661,7 @@ void FixAveGrid::normalize_atom(int numsamples)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
count = count2d_sample[iy][ix];
if (count) {
for (m = 0; m <= nvalues; m++) {
for (m = 0; m < nvalues; m++) {
if (which[m] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[m] == ArgInfo::DENSITY_MASS)
@ -1551,7 +1705,7 @@ void FixAveGrid::normalize_atom(int numsamples)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
count = count3d_sample[iz][iy][ix];
if (count) {
for (m = 0; m <= nvalues; m++) {
for (m = 0; m < nvalues; m++) {
if (which[m] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[m] == ArgInfo::DENSITY_MASS)
@ -1641,8 +1795,6 @@ void FixAveGrid::pack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *lis
}
} else {
for (i = 0; i < nlist; i++) {
printf("PACK i %d nlist %d, listI %d nvalues %d count %d\n",
i,nlist,list[i],nvalues,count[list[i]]);
buf[m++] = count[list[i]];
values = &data[nvalues*list[i]];
for (j = 0; j < nvalues; j++)

6
src/fix_ave_grid.h
View File

@ -113,9 +113,9 @@ class FixAveGrid : public Fix {
double ***, double ***, double ****);
void sum_sample_to_epoch();
void copy_epoch_to_sample();
void sum_sample_to_running() {}
void copy_sample_to_output() {}
void copy_running_to_output() {}
void sum_sample_to_running();
void copy_sample_to_output();
void copy_running_to_output();
void copy_sample_to_window(int) {}
void subtract_window_from_running() {}

11
src/grid2d.cpp
View File

@ -366,7 +366,16 @@ void Grid2d::get_box(int dim, double &lo, double &delta)
delta = prd[dim] / ngrid[dim];
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
return sizes of two buffers needed for communication
either on regular grid or procs or irregular tiling
nbuf1 = largest pack or unpack in any Send or Recv or Copy
nbuf2 = larget of sum of all packs or unpacks in Send or Recv
for regular comm, nbuf1 = nbuf2
for irregular comm, nbuf2 >= nbuf2
nbuf1,nbuf2 are just count of grid points
caller converts them to message size for grid data it stores
------------------------------------------------------------------------- */
void Grid2d::setup(int &nbuf1, int &nbuf2)
{

11
src/grid3d.cpp
View File

@ -399,7 +399,16 @@ void Grid3d::get_box(int dim, double &lo, double &delta)
delta = prd[dim] / ngrid[dim];
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
return sizes of two buffers needed for communication
either on regular grid or procs or irregular tiling
nbuf1 = largest pack or unpack in any Send or Recv or Copy
nbuf2 = larget of sum of all packs or unpacks in Send or Recv
for regular comm, nbuf1 = nbuf2
for irregular comm, nbuf2 >= nbuf2
nbuf1,nbuf2 are just count of grid points
caller converts them to message size for grid data it stores
------------------------------------------------------------------------- */
void Grid3d::setup(int &nbuf1, int &nbuf2)
{