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add support for discard yes/no of out-of-bin atoms

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This commit is contained in:
Steve Plimpton
2022-08-30 12:49:09 -06:00
parent 6b093cb80a
commit ac2cf8c4ed
5 changed files with 74 additions and 29 deletions
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63
src/fix_ave_grid.cpp
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@ -36,6 +36,7 @@ using namespace FixConst;
enum{ALL,SAMPLE,NONORM};
enum{ONE,RUNNING,WINDOW};
enum{DISCARD,KEEP};
// OFFSET avoids outside-of-box atoms being rounded to grid pts incorrectly
// SHIFT = 0.0 assigns atoms to lower-left grid pt
@ -166,6 +167,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
// optional args
discardflag = DISCARD;
normflag = ALL;
aveflag = ONE;
nwindow = 0;
@ -175,7 +177,14 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
cdof = 0.0;
while (iarg < nargnew) {
if (strcmp(arg[iarg],"norm") == 0) {
if (strcmp(arg[iarg],"discard") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command");
if (strcmp(arg[iarg+1],"yes") == 0) discardflag = DISCARD;
else if (strcmp(arg[iarg+1],"no") == 0) discardflag = KEEP;
else error->all(FLERR,"Illegal fix ave/grid command");
iarg += 2;
} else if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command");
if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL;
else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE;
@ -794,10 +803,18 @@ void FixAveGrid::atom2grid()
{
int i,j,m,n,ix,iy,iz;
double **count2d = grid_sample->count2d;
double **vec2d = grid_sample->vec2d;
double ***array2d = grid_sample->array2d;
double ***count3d = grid_sample->count3d;
double ***vec3d = grid_sample->vec3d;
double ****array3d = grid_sample->array3d;
// bin[i][dim] = indices of bin each atom is in
// not set if group mask does not match
// also count atoms contributing to each bin
// skip atom if group mask does not match
// check if any atom is out of bounds for my local grid
// for nonperiodic dim, remap atom to first/last bin if out of bounds
// count atoms contributing to each bin
double *boxlo,*prd;
int *periodicity = domain->periodicity;
@ -826,13 +843,6 @@ void FixAveGrid::atom2grid()
memory->create(skip,maxatom,"ave/grid:skip");
}
double **count2d = grid_sample->count2d;
double **vec2d = grid_sample->vec2d;
double ***array2d = grid_sample->array2d;
double ***count3d = grid_sample->count3d;
double ***vec3d = grid_sample->vec3d;
double ****array3d = grid_sample->array3d;
if (triclinic) domain->x2lamda(nlocal);
int flag = 0;
@ -850,12 +860,20 @@ void FixAveGrid::atom2grid()
if (ix < nxlo_out || ix > nxhi_out) {
if (periodicity[0]) flag = 1;
else skip[i] = 1;
else if (discardflag == KEEP) {
if (ix < nxlo_out && nxlo_out == 0) ix = 0;
else if (ix > nxhi_out && nxhi_out == nxgrid-1) ix = nxgrid-1;
else flag = 1;
} else skip[i] = 1;
continue;
}
if (iy < nylo_out || iy > nyhi_out) {
if (periodicity[1]) flag = 1;
else skip[i] = 1;
else if (discardflag == KEEP) {
if (iy < nylo_out && nylo_out == 0) iy = 0;
else if (iy > nyhi_out && nyhi_out == nygrid-1) iy = nygrid-1;
else flag = 1;
} else skip[i] = 1;
continue;
}
@ -878,17 +896,30 @@ void FixAveGrid::atom2grid()
if (ix < nxlo_out || ix > nxhi_out) {
if (periodicity[0]) flag = 1;
else skip[i] = 1;
continue;
else if (discardflag == KEEP) {
if (ix < nxlo_out && nxlo_out == 0) ix = 0;
else if (ix > nxhi_out && nxhi_out == nxgrid-1) ix = nxgrid-1;
else flag = 1;
} else skip[i] = 1;
}
if (iy < nylo_out || iy > nyhi_out) {
if (periodicity[1]) flag = 1;
else skip[i] = 1;
else if (discardflag == KEEP) {
if (iy < nylo_out && nylo_out == 0) iy = 0;
else if (iy > nyhi_out && nyhi_out == nygrid-1) iy = nygrid-1;
else flag = 1;
} else skip[i] = 1;
continue;
}
if (iz < nzlo_out || iz > nzhi_out) {
if (periodicity[2]) flag = 1;
else skip[i] = 1;
else if (discardflag == KEEP) {
if (iz < nzlo_out && nzlo_out == 0) iz = 0;
else if (iz > nzhi_out && nzhi_out == nzgrid-1) iz = nzgrid-1;
else flag = 1;
} else skip[i] = 1;
continue;
}