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debugging fixes

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This commit is contained in:
Steve Plimpton
2022-08-03 17:43:04 -06:00
parent c3d563ca39
commit c44794730b
6 changed files with 56 additions and 31 deletions
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77
src/fix_ave_grid.cpp
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@ -50,6 +50,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
which(nullptr), argindex(nullptr), ids(nullptr),
value2index(nullptr), value2grid(nullptr), value2data(nullptr),
grid2d(nullptr), grid3d(nullptr),
grid_buf1(nullptr), grid_buf2(nullptr),
vec2d(nullptr), array2d(nullptr), vec3d(nullptr), array3d(nullptr),
count2d(nullptr), count3d(nullptr)
{
@ -154,10 +155,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix ave/grid cannot use variable for grid info");
nvalues++;
// unrecognized arg (option)
} else break;
}
iarg++;
}
@ -286,6 +284,9 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
char *idcompute,*gname,*dname;
utils::grid_parse(FLERR,ids[i],idcompute,gname,dname,error);
delete [] ids[i];
ids[i] = new char[strlen(idcompute)+1];
strcpy(ids[i],idcompute);
Compute *icompute = modify->get_compute_by_id(idcompute);
if (!icompute)
@ -323,8 +324,8 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
"Fix ave/grid compute {} array {} is accessed out-of-range",
idcompute,dname);
value2grid[iarg] = igrid;
value2data[iarg] = idata;
value2grid[i] = igrid;
value2data[i] = idata;
delete [] idcompute;
delete [] gname;
@ -334,6 +335,9 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
char *idfix,*gname,*dname;
utils::grid_parse(FLERR,ids[i],idfix,gname,dname,error);
delete [] ids[i];
ids[i] = new char[strlen(idfix)+1];
strcpy(ids[i],idfix);
Fix *ifix = modify->get_fix_by_id(idfix);
if (!ifix) error->all(FLERR,"Could not find fix ave/grid fix ID: {}",
@ -372,8 +376,8 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
"Fix ave/grid compute {} array {} is accessed out-of-range",
idfix,dname);
value2grid[iarg] = igrid;
value2data[iarg] = idata;
value2grid[i] = igrid;
value2data[i] = idata;
delete [] idfix;
delete [] gname;
@ -483,6 +487,7 @@ FixAveGrid::~FixAveGrid()
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->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);
@ -510,19 +515,19 @@ void FixAveGrid::init()
if (which[m] == ArgInfo::COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
error->all(FLERR,"Compute ID for fix ave/grid does not exist");
value2index[m] = icompute;
} else if (which[m] == ArgInfo::FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
error->all(FLERR,"Fix ID for fix ave/grid does not exist");
value2index[m] = ifix;
} else if (which[m] == ArgInfo::VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/atom does not exist");
error->all(FLERR,"Variable name for fix ave/grid does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@ -598,20 +603,22 @@ void FixAveGrid::end_of_step()
// 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 ?
if (irepeat == 0) zero_grid();
if (modeatom) {
if (dimension == 2) {
if (ngridout) memcpy(&count2d[0][0],0,ngridout*sizeof(int));
if (ngridout) memset(&count2d[nylo_out][nxlo_out],0,
ngridout*sizeof(double));
} else {
if (ngridout) memcpy(&count3d[0][0][0],0,ngridout*sizeof(int));
if (ngridout) memset(&count3d[nzlo_out][nylo_out][nxlo_out],0,
ngridout*sizeof(double));
}
}
// ATOM mode
// accumulate per-atom attributes,computes,fixes,variables to local grid
// set local per-grid values for either ATOM or GRID mode
// per-atom compute/fix/variable may invoke computes so wrap with clear/add
@ -633,7 +640,7 @@ void FixAveGrid::end_of_step()
}
irepeat = 0;
nvalid = ntimestep+peratom_freq - ((bigint) nrepeat-1)*nevery;
nvalid = ntimestep+pergrid_freq - ((bigint) nrepeat-1)*nevery;
if (modeatom) modify->addstep_compute(nvalid);
// ghost to owned grid communication for atom mode
@ -720,7 +727,7 @@ void FixAveGrid::atom2grid()
if (!(mask[i] & groupbit)) continue;
ix = static_cast<int> ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET;
iy = static_cast<int> ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET;
count2d[iy][ix]++;
count2d[iy][ix] += 1.0;
bin[i][0] = iy;
bin[i][1] = ix;
}
@ -730,7 +737,7 @@ void FixAveGrid::atom2grid()
ix = static_cast<int> ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET;
iy = static_cast<int> ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET;
iz = static_cast<int> ((x[i][2]-boxlo[2])*dzinv + shift) - OFFSET;
count3d[iz][iy][ix]++;
count3d[iz][iy][ix] += 1.0;
bin[i][0] = iz;
bin[i][1] = iy;
bin[i][2] = ix;
@ -940,9 +947,9 @@ void FixAveGrid::grid2grid()
else
oarray3d = (double ****) compute->get_griddata_by_index(idata);
} else {
if (j == 0)
if (j == 0) {
ovec3d = (double ***) fix->get_griddata_by_index(idata);
else
} else
oarray3d = (double ****) fix->get_griddata_by_index(idata);
}
@ -985,15 +992,19 @@ void FixAveGrid::zero_grid()
{
if (dimension == 2) {
if (nvalues == 1) {
if (ngridout) memcpy(&vec2d[0][0],0,ngridout*sizeof(double));
if (ngridout) memset(&vec2d[nylo_out][nxlo_out],0,
ngridout*sizeof(double));
} else {
if (ngridout) memcpy(&array2d[0][0][0],0,ngridout*nvalues*sizeof(double));
if (ngridout) memset(&array2d[nylo_out][nxlo_out][0],0,
ngridout*nvalues*sizeof(double));
}
} else {
if (nvalues == 1) {
if (ngridout) memcpy(&vec3d[0][0][0],0,ngridout*sizeof(double));
if (ngridout) memset(&vec3d[nzlo_out][nylo_out][nxlo_out],0,
ngridout*sizeof(double));
} else {
if (ngridout) memcpy(&array3d[0][0][0][0],0,ngridout*nvalues*sizeof(double));
if (ngridout) memset(&array3d[nzlo_out][nylo_out][nxlo_out][0],0,
ngridout*nvalues*sizeof(double));
}
}
}
@ -1027,6 +1038,7 @@ void *FixAveGrid::get_grid_by_index(int index)
if (dimension == 2) return grid2d;
else return grid3d;
}
return nullptr;
}
@ -1047,6 +1059,10 @@ int FixAveGrid::get_griddata_by_name(int igrid, char *name, int &ncol)
else ncol = nvalues;
return 0;
}
if (igrid == 0 && strcmp(name,"count") == 0) {
ncol = 0;
return 1;
}
return -1;
}
@ -1068,6 +1084,11 @@ void *FixAveGrid::get_griddata_by_index(int index)
else return array3d;
}
}
if (index == 1) {
if (dimension == 2) return count2d;
else return count3d;
}
return nullptr;
}
@ -1090,11 +1111,11 @@ double FixAveGrid::memory_usage()
bigint FixAveGrid::nextvalid()
{
bigint nvalid = (update->ntimestep/peratom_freq)*peratom_freq + peratom_freq;
if (nvalid-peratom_freq == update->ntimestep && nrepeat == 1)
bigint nvalid = (update->ntimestep/pergrid_freq)*pergrid_freq + pergrid_freq;
if (nvalid-pergrid_freq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= ((bigint)nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += peratom_freq;
if (nvalid < update->ntimestep) nvalid += pergrid_freq;
return nvalid;
}