CarpetIOHDF5: fix way hyperslab is computed

  to compute the hyperslab one needs to base its location on the extent of the
  data in memory not in the extent that we want to output.

1 files changed, 15 insertions, 4 deletions

diff --git a/Carpet/CarpetIOHDF5/src/OutputSlice.cc b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
index c503b95f0..4ee4ffe26 100644
--- a/Carpet/CarpetIOHDF5/src/OutputSlice.cc
+++ b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
@@ -1319,10 +1319,19 @@ namespace CarpetIOHDF5 {
 
     if (not diagonal_output) { // not outputting the diagonal
 
+      // there are currently three "extent" variables in use:
+      // data_ext - the extent of the component in memory 
+      // gfext    - the bounding box of data to be written
+      // ext      - gfext in the output dimension(s)
+      // data_ext and gfext are used to construct the hyperslab location and
+      // size, ext is just a shorthand.
+      // TODO: maybe transfer only ext instead of data_ext in copy_from
       const vect<int,outdim> lo = gfext.lower()[dirs];
       const vect<int,outdim> up = gfext.upper()[dirs];
       const vect<int,outdim> str = gfext.stride()[dirs];
       const bbox<int,outdim> ext(lo,up,str);
+      const dh* const dd = arrdata.at(gi).at(m).dd;
+      const ibbox& data_ext = dd->light_boxes.at(ml).at(rl).at(c).exterior;
 
       // Check whether the output origin is contained in the extent of
       // the data that should be output
@@ -1335,19 +1344,21 @@ namespace CarpetIOHDF5 {
       vector<hsize_t> mem_shape(dim);
       vector<hsize_t> slice_shape(rank, 1);
       for (int d = 0; d < dim; d++) {
-        mem_shape[dim-1-d] = gfext.shape()[d] / gfext.stride()[d];
+        mem_shape[dim-1-d] = data_ext.shape()[d] / data_ext.stride()[d];
         if (d < outdim) {
           slice_shape[outdim-1-d] = ext.shape()[d] / ext.stride()[d];
         }
       }
 
-      ivect slice_lower(org - gfext.lower());
+      ivect slice_lower(org - data_ext.lower());
       for (int d = 0; d < outdim; d++) {
-        slice_lower[dirs[d]] = 0;
+        slice_lower[dirs[d]] = ext.lower()[d] - 
+                               data_ext.lower()[dirs[d]];
       }
       ivect slice_upper(slice_lower);
       for (int d = 0; d < outdim; d++) {
-        slice_upper[dirs[d]] = ext.upper()[d] - ext.lower()[d];
+        slice_upper[dirs[d]] = ext.upper()[d] - 
+                               data_ext.lower()[dirs[d]];
       }
       slice_lower /= gfext.stride();
       slice_upper /= gfext.stride();