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debugging fixes

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This commit is contained in:
Steve Plimpton
2022-08-22 17:13:59 -06:00
parent b26ee6d75d
commit 37e9bf54ab
3 changed files with 192 additions and 63 deletions
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16
src/compute_property_grid.cpp
View File

@ -298,7 +298,7 @@ double ComputePropertyGrid::memory_usage()
void ComputePropertyGrid::pack_id(int n)
{
if (dimension == 2) {
if (nvalues == 0) {
if (nvalues == 1) {
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) vec2d[iy][ix] = iy * nxgrid + ix + 1;
} else {
@ -306,7 +306,7 @@ void ComputePropertyGrid::pack_id(int n)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) array2d[iy][ix][n] = iy * nxgrid + ix + 1;
}
} else if (dimension == 3) {
if (nvalues == 0) {
if (nvalues == 1) {
for (int iz = nzlo_in; iz <= nzhi_in; iz++)
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++)
@ -327,7 +327,7 @@ void ComputePropertyGrid::pack_id(int n)
template <int IDIM> void ComputePropertyGrid::pack_indices(int n)
{
if (dimension == 2) {
if (nvalues == 0) {
if (nvalues == 1) {
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
if (IDIM == 0) vec2d[iy][ix] = ix + 1;
@ -342,7 +342,7 @@ template <int IDIM> void ComputePropertyGrid::pack_indices(int n)
}
} else if (dimension == 3) {
if (nvalues == 0) {
if (nvalues == 1) {
for (int iz = nzlo_in; iz <= nzhi_in; iz++)
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
@ -387,7 +387,7 @@ template <int POS, int MODE, int IDIM> void ComputePropertyGrid::pack_coords(int
if (IDIM == 1) delta = 1.0 / nygrid;
}
if (nvalues == 0) {
if (nvalues == 1) {
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
if (POS == LOW) {
@ -422,7 +422,7 @@ template <int POS, int MODE, int IDIM> void ComputePropertyGrid::pack_coords(int
double dy = 1.0 / nygrid;
lamda[2] = 0.0;
if (nvalues == 0) {
if (nvalues == 1) {
for (int iy = nylo_in; iy <= nyhi_in; iy++) {
lamda[1] = iy * dy;
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
@ -462,7 +462,7 @@ template <int POS, int MODE, int IDIM> void ComputePropertyGrid::pack_coords(int
if (IDIM == 2) delta = 1.0 / nzgrid;
}
if (nvalues == 0) {
if (nvalues == 1) {
for (int iz = nzlo_in; iz <= nzhi_in; iz++)
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
@ -503,7 +503,7 @@ template <int POS, int MODE, int IDIM> void ComputePropertyGrid::pack_coords(int
double dy = 1.0 / nygrid;
double dz = 1.0 / nzgrid;
if (nvalues == 0) {
if (nvalues == 1) {
for (int iz = nzlo_in; iz <= nzhi_in; iz++) {
lamda[2] = iz * dz;
for (int iy = nylo_in; iy <= nyhi_in; iy++) {

237
src/fix_ave_grid.cpp
View File

@ -53,7 +53,13 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
grid2d(nullptr), grid3d(nullptr),
grid_buf1(nullptr), grid_buf2(nullptr),
vec2d(nullptr), vec3d(nullptr), array2d(nullptr), array3d(nullptr),
count2d(nullptr), count3d(nullptr)
count2d(nullptr), count3d(nullptr),
vec2d_sample(nullptr), vec3d_sample(nullptr), array2d_sample(nullptr), array3d_sample(nullptr),
count2d_sample(nullptr), count3d_sample(nullptr),
vec2d_epoch(nullptr), vec3d_epoch(nullptr), array2d_epoch(nullptr), array3d_epoch(nullptr),
count2d_epoch(nullptr), count3d_epoch(nullptr),
vec2d_running(nullptr), vec3d_running(nullptr), array2d_running(nullptr), array3d_running(nullptr),
count2d_running(nullptr), count3d_running(nullptr)
{
if (narg < 10) error->all(FLERR,"Illegal fix ave/grid command");
@ -97,45 +103,45 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 1;
argindex[nvalues] = 1;
modeatom = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 2;
argindex[nvalues] = 2;
modeatom = 1;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 1;
argindex[nvalues] = 1;
modeatom = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 2;
argindex[nvalues] = 2;
modeatom = 1;
} else if (strcmp(arg[iarg],"density/number") == 0) {
which[nvalues] = ArgInfo::DENSITY_NUMBER;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
which[nvalues] = ArgInfo::DENSITY_MASS;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else if (strcmp(arg[iarg],"mass") == 0) {
which[nvalues] = ArgInfo::MASS;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else if (strcmp(arg[iarg],"temp") == 0) {
which[nvalues] = ArgInfo::TEMPERATURE;
argindex[nvalues++] = 0;
argindex[nvalues] = 0;
modeatom = 1;
} else {
@ -154,10 +160,9 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
if (modegrid && which[nvalues] == ArgInfo::VARIABLE)
error->all(FLERR,"Fix ave/grid cannot use variable for grid info");
nvalues++;
}
nvalues++;
iarg++;
}
@ -387,18 +392,18 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
// instantiate the Grid class and allocate per-grid memory
double maxdist,shift;
double maxdist;
if (modeatom) {
maxdist = 0.5 * neighbor->skin;
shift = SHIFT;
shift = OFFSET + SHIFT;
} else if (modegrid) {
maxdist = 0.0;
shift = 0.0;
}
if (dimension == 2) {
grid2d = new Grid2d(lmp, world, nxgrid, nygrid, maxdist, 0, shift,
grid2d = new Grid2d(lmp, world, nxgrid, nygrid, maxdist, 0, SHIFT,
nxlo_in, nxhi_in, nylo_in, nyhi_in,
nxlo_out, nxhi_out, nylo_out, nyhi_out);
@ -408,19 +413,8 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1);
if (nvalues == 1)
memory->create2d_offset(vec2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec2d");
else
memory->create3d_offset_last(array2d, nylo_out, nyhi_out, nxlo_out,
nxhi_out, nvalues, "ave/grid:array2d");
if (modeatom)
memory->create2d_offset(count2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count2d");
} else {
grid3d = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid, maxdist, 0, shift,
grid3d = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid, maxdist, 0, SHIFT,
nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in,
nxlo_out, nxhi_out, nylo_out, nyhi_out,
nzlo_out, nzhi_out);
@ -431,22 +425,12 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) *
(nzhi_out - nzlo_out + 1);
if (nvalues == 1)
memory->create3d_offset(vec3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d");
else
memory->create4d_offset_last(array3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out, nvalues,
"ave/grid:array3d");
if (modeatom)
memory->create3d_offset(count3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d");
}
// allocate all per-grid data
allocate_grid();
// zero the output grid and counts since dump may access it on timestep 0
// zero running grid if used by ave
@ -459,12 +443,13 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
if (aveflag == RUNNING || aveflag == WINDOW)
zero_grid(count2d_running,vec2d_running,array2d_running,
count3d_running,vec3d_running,array3d_running);
// bin indices for ATOM mode
// bin indices and skip flags for ATOM mode
// vresult for per-atom variable evaluation
maxatom = 0;
bin = nullptr;
skip = nullptr;
maxvar = 0;
vresult = nullptr;
@ -494,19 +479,19 @@ FixAveGrid::~FixAveGrid()
delete grid2d;
delete grid3d;
memory->destroy(grid_buf1);
memory->destroy(grid_buf2);
memory->destroy2d_offset(vec2d,nylo_out,nxlo_out);
memory->destroy2d_offset(array2d,nylo_out,nxlo_out);
memory->destroy2d_offset(count2d,nylo_out,nxlo_out);
// deallocate all per-grid data
memory->destroy3d_offset(vec3d,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);
deallocate_grid();
memory->destroy(bin);
memory->destroy(vresult);
if (modeatom) {
memory->destroy(bin);
memory->destroy(skip);
memory->destroy(vresult);
}
}
/* ---------------------------------------------------------------------- */
@ -628,7 +613,7 @@ void FixAveGrid::end_of_step()
if (irepeat == 0) zero_grid(count2d_sample,vec2d_sample,array2d_sample,
count3d_sample,vec3d_sample,array3d_sample);
if (irepeat == 0 || normflag == SAMPLE)
if (irepeat == 0 && normflag == SAMPLE)
zero_grid(count2d_epoch,vec2d_epoch,array2d_epoch,
count3d_epoch,vec3d_epoch,array3d_epoch);
@ -781,6 +766,7 @@ void FixAveGrid::atom2grid()
}
if (triclinic) domain->x2lamda(nlocal);
int flag = 0;
if (dimension == 2) {
@ -846,6 +832,7 @@ void FixAveGrid::atom2grid()
}
if (flag) error->one(FLERR,"Out of range fix ave/grid atoms");
if (triclinic) domain->lamda2x(nlocal);
// loop over user-specified values
@ -1199,6 +1186,144 @@ void FixAveGrid::grid2grid()
}
}
/* ----------------------------------------------------------------------
allocate all grids which will be used
if ATOM mode, also allocate per-cell counts
------------------------------------------------------------------------- */
void FixAveGrid::allocate_grid()
{
if (dimension == 2) {
if (nvalues == 1) {
memory->create2d_offset(vec2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec2d");
memory->create2d_offset(vec2d_sample, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec2d_sample");
if (normflag == SAMPLE)
memory->create2d_offset(vec2d_epoch, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec2d_epoch");
if (aveflag == RUNNING)
memory->create2d_offset(vec2d_running, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec2d_running");
} else {
memory->create3d_offset_last(array2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d");
memory->create3d_offset_last(array2d_sample, nylo_out, nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_sample");
if (normflag == SAMPLE)
memory->create3d_offset_last(array2d_epoch, nylo_out, nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_epoch");
if (aveflag == RUNNING)
memory->create3d_offset_last(array2d_running, nylo_out, nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_running");
}
if (modeatom) {
memory->create2d_offset(count2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count2d");
memory->create2d_offset(count2d_sample, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count2d_sample");
if (normflag == SAMPLE)
memory->create2d_offset(count2d_epoch, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count2d_epoch");
if (normflag == RUNNING) {
memory->create2d_offset(count2d_running, nylo_out, nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count2d_running");
}
}
} else if (dimension == 3) {
if (nvalues == 1) {
memory->create3d_offset(vec3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d");
memory->create3d_offset(vec3d_sample, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d_sample");
if (normflag == SAMPLE)
memory->create3d_offset(vec3d_epoch, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d_epoch");
if (aveflag == RUNNING)
memory->create3d_offset(vec3d_running, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:vec3d_running");
} else {
memory->create4d_offset_last(array3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out, nvalues,
"ave/grid:array3d");
memory->create4d_offset_last(array3d_sample, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_sample");
if (normflag == SAMPLE)
memory->create4d_offset_last(array3d_epoch, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_epoch");
if (aveflag == RUNNING)
memory->create4d_offset_last(array3d_running, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
nvalues, "ave/grid:array3d_running");
}
if (modeatom) {
memory->create3d_offset(count3d, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out, "ave/grid:count3d");
memory->create3d_offset(count3d_sample, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count3d_sample");
if (normflag == SAMPLE)
memory->create3d_offset(count3d_epoch, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count3d_epoch");
if (normflag == RUNNING)
memory->create3d_offset(count3d_running, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out,
"ave/grid:count3d_running");
}
}
}
/* ----------------------------------------------------------------------
deallocate all grids and counts
------------------------------------------------------------------------- */
void FixAveGrid::deallocate_grid()
{
memory->destroy2d_offset(vec2d,nylo_out,nxlo_out);
memory->destroy2d_offset(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->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->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->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->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->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->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->destroy3d_offset(count3d_running,nzlo_out,nylo_out,nxlo_out);
}
/* ----------------------------------------------------------------------
zero values for a grid incluing ghost cells
if ATOM mode, also zero per-cell counts
@ -1516,9 +1641,11 @@ 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++)
for (j = 0; j < nvalues; j++)
buf[m++] = values[j];
}
}
@ -1556,7 +1683,7 @@ void FixAveGrid::unpack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *l
for (i = 0; i < nlist; i++) {
count[list[i]] = buf[m++];
values = &data[nvalues*list[i]];
for (j = 0; j <= nvalues; j++)
for (j = 0; j < nvalues; j++)
values[j] = buf[m++];
}
}

2
src/fix_ave_grid.h
View File

@ -107,6 +107,8 @@ class FixAveGrid : public Fix {
void atom2grid();
void grid2grid();
void allocate_grid();
void deallocate_grid();
void zero_grid(double **, double **, double ***,
double ***, double ***, double ****);
void sum_sample_to_epoch();