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

doc/src/fix_ave_grid.rst

@@ -42,10 +42,13 @@ Syntax
        f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below)
 
 * zero or more keyword/arg pairs may be appended
-* keyword = *norm* or *ave* or *bias* or *adof* or *cdof*
+* keyword = *discard* or *norm* or *ave* or *bias* or *adof* or *cdof*
 
   .. parsed-literal::
 
+       *discard* arg = *yes* or *no*
+         yes = discard an atom outside grid in a non-periodic dimension
+         no = remap an atom outside grid in a non-periodic dimension to first or last grid cell
        *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized
          all = output is sum of atoms across all *Nrepeat* samples, divided by atom count
          sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat*
@@ -296,6 +299,17 @@ Additional optional keywords also affect the operation of this fix and
 its outputs.  Some are only applicable to per-atom mode.  Some are
 applicable to both per-atom and per-grid mode.
 
+The *discard* keyword is only applicable to per-atom mode.  If a
+dimension of the system is non-periodic, then grid cells will only
+span the box dimension (fixed or shrink-wrap boundaries as set by the
+:doc:`boundary` command).  An atom may thus be slighlty outside the
+range of grid cells on a particular timestep.  If *discard* is set to
+*yes* (the default), then the atom will be assigned to the closest
+grid cell (lowest or highest) in that dimension.  If *discard* is set
+to *no* the atom will be ignored.
+ 
+----------
+
 The *norm* keyword is only applicable to per-atom mode.  In per-grid
 mode, the *norm* keyword setting is ignored.  The output grid value on
 an *Nfreq* timestep is the sum of the grid values in each of the

src/fix_ave_grid.cpp

@@ -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
+  // skip atom if group mask does not match
-  // also count atoms contributing to each bin
   // 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;
+        else if (discardflag == KEEP) {
-        continue;
+          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;
       }
 

src/fix_ave_grid.h

@@ -51,7 +51,7 @@ class FixAveGrid : public Fix {
   int nrepeat, irepeat;
   bigint nvalid, nvalid_last;
   int modeatom, modegrid;
-  int normflag,aveflag,nwindow;
+  int discardflag, normflag, aveflag, nwindow;
 
   int running_count;
   int window_count,window_oldest,window_newest;

src/grid2d.cpp

@@ -129,13 +129,13 @@ Grid2d::Grid2d(LAMMPS *lmp, MPI_Comm gcomm,
   int *periodicity = domain->periodicity;
 
   if (!periodicity[0]) {
-    oxlo = MAX(1,oxlo);
+    oxlo = MAX(0,oxlo);
-    oxhi = MIN(gnx-1,oxhi);
+    oxhi = MIN(nx-1,oxhi);
   }
 
   if (!periodicity[1]) {
-    oylo = MAX(1,oylo);
+    oylo = MAX(0,oylo);
-    oyhi = MIN(gnx-1,oyhi);
+    oyhi = MIN(ny-1,oyhi);
   }
 
   // error check on size of grid stored by this proc

src/grid3d.cpp

@@ -135,18 +135,18 @@ Grid3d::Grid3d(LAMMPS *lmp, MPI_Comm gcomm,
   int *periodicity = domain->periodicity;
 
   if (!periodicity[0]) {
-    oxlo = MAX(1,oxlo);
+    oxlo = MAX(0,oxlo);
-    oxhi = MIN(gnx-1,oxhi);
+    oxhi = MIN(nx-1,oxhi);
   }
 
   if (!periodicity[1]) {
-    oylo = MAX(1,oylo);
+    oylo = MAX(0,oylo);
-    oyhi = MIN(gnx-1,oyhi);
+    oyhi = MIN(ny-1,oyhi);
   }
 
   if (!periodicity[2]) {
-    ozlo = MAX(1,ozlo);
+    ozlo = MAX(0,ozlo);
-    ozhi = MIN(gnx-1,ozhi);
+    ozhi = MIN(nz-1,ozhi);
   }
 
   // error check on size of grid stored by this proc