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-rw-r--r--Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc4
-rw-r--r--Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh2
-rw-r--r--Carpet/CarpetIOHDF5/src/Input.cc36
-rw-r--r--Carpet/CarpetIOHDF5/src/Output.cc12
-rw-r--r--Carpet/CarpetIOHDF5/src/OutputSlice.cc9
5 files changed, 54 insertions, 9 deletions
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index d4abcccbd..1305a49d1 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -299,6 +299,8 @@ int AddSliceAttributes(const cGH* const cctkGH,
const vector<double>& origin,
const vector<double>& delta,
const vector<int>& iorigin,
+ const vector<int>& ioffset,
+ const vector<int>& ioffsetdenom,
const vector<int>& bbox,
const vector<int>& nghostzones,
hid_t& dataset)
@@ -314,6 +316,8 @@ int AddSliceAttributes(const cGH* const cctkGH,
error_count += WriteAttribute(dataset, "origin", &origin[0], origin.size());
error_count += WriteAttribute(dataset, "delta", &delta[0], delta.size());
error_count += WriteAttribute(dataset, "iorigin", &iorigin[0], iorigin.size());
+ error_count += WriteAttribute(dataset, "ioffset", &ioffset[0], ioffset.size());
+ error_count += WriteAttribute(dataset, "ioffsetdenom", &ioffsetdenom[0], ioffsetdenom.size());
// bbox and nghostzones are only used for grid functions and grid arrays
if (bbox.size() > 0) {
error_count += WriteAttribute(dataset, "cctk_bbox", &bbox[0], bbox.size());
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
index e8f44e9b9..dfa6a276e 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
@@ -140,6 +140,8 @@ namespace CarpetIOHDF5
const vector<double>& origin,
const vector<double>& delta,
const vector<int>& iorigin,
+ const vector<int>& ioffset,
+ const vector<int>& ioffsetdenom,
const vector<int>& bbox,
const vector<int>& nghostzones,
hid_t& dataset);
diff --git a/Carpet/CarpetIOHDF5/src/Input.cc b/Carpet/CarpetIOHDF5/src/Input.cc
index 21c61cea8..cb0e57040 100644
--- a/Carpet/CarpetIOHDF5/src/Input.cc
+++ b/Carpet/CarpetIOHDF5/src/Input.cc
@@ -35,6 +35,8 @@ typedef struct {
int component;
int rank;
ivect iorigin;
+ ivect ioffset;
+ ivect ioffsetdenom;
vector<hsize_t> shape;
} patch_t;
@@ -1058,9 +1060,6 @@ static herr_t BrowseDatasets (hid_t group, const char *objectname, void *arg)
HDF5_ERROR (attr = H5Aopen_name (dataset, "group_timelevel"));
HDF5_ERROR (H5Aread (attr, H5T_NATIVE_INT, &patch.timelevel));
HDF5_ERROR (H5Aclose (attr));
- // in old days (before February 2005)
- // timelevels were stored as negative numbers
- patch.timelevel = abs (patch.timelevel);
HDF5_ERROR (attr = H5Aopen_name (dataset, "iorigin"));
HDF5_ERROR (dataspace = H5Aget_space (attr));
assert (H5Sget_simple_extent_npoints (dataspace) == patch.rank);
@@ -1068,6 +1067,25 @@ static herr_t BrowseDatasets (hid_t group, const char *objectname, void *arg)
patch.iorigin = 0;
HDF5_ERROR (H5Aread (attr, H5T_NATIVE_INT, &patch.iorigin[0]));
HDF5_ERROR (H5Aclose (attr));
+ patch.ioffset = 0;
+ attr = H5Aopen_name (dataset, "ioffset");
+ // ioffset and ioffsetdenom may not be present; if so, use a default
+ if (attr >= 0) {
+ HDF5_ERROR (dataspace = H5Aget_space (attr));
+ assert (H5Sget_simple_extent_npoints (dataspace) == patch.rank);
+ HDF5_ERROR (H5Sclose (dataspace));
+ HDF5_ERROR (H5Aread (attr, H5T_NATIVE_INT, &patch.ioffset[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ }
+ patch.ioffsetdenom = 1;
+ attr = H5Aopen_name (dataset, "ioffsetdenom");
+ if (attr >= 0) {
+ HDF5_ERROR (dataspace = H5Aget_space (attr));
+ assert (H5Sget_simple_extent_npoints (dataspace) == patch.rank);
+ HDF5_ERROR (H5Sclose (dataspace));
+ HDF5_ERROR (H5Aread (attr, H5T_NATIVE_INT, &patch.ioffsetdenom[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ }
HDF5_ERROR (H5Dclose (dataset));
// try to obtain the map and component number from the patch's name
@@ -1141,9 +1159,15 @@ static int ReadVar (const cGH* const cctkGH,
}
const hid_t datatype = CCTKtoHDF5_Datatype (cctkGH, group.vartype, 0);
- const ivect stride = group.grouptype == CCTK_GF ?
- maxspacereflevelfact/spacereflevelfact : 1;
- ivect lower = patch->iorigin * stride;
+ centering const refcent = vhh.at(0)->refcent;
+ int const reffactdenom =
+ group.grouptype == CCTK_GF ?
+ (refcent == vertex_centered ? 1 : 2) : 1;
+ const ivect stride =
+ group.grouptype == CCTK_GF ?
+ reffactdenom * maxspacereflevelfact / spacereflevelfact : 1;
+ assert (all (stride % patch->ioffsetdenom == 0));
+ ivect lower = patch->iorigin * stride + patch->ioffset * stride / patch->ioffsetdenom;
ivect upper = lower + (shape - 1) * stride;
// Traverse all local components on all maps
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index 3c44d87ac..1b5bf8eec 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -809,7 +809,17 @@ static int AddAttributes (const cGH *const cctkGH, const char *fullname,
HDF5_ERROR (H5Aclose (attr));
}
- ivect iorigin = bbox.lower() / bbox.stride();
+ ivect const ioffsetdenom = bbox.stride();
+ HDF5_ERROR (attr = H5Acreate (dataset, "ioffsetdenom", H5T_NATIVE_INT,
+ dataspace, H5P_DEFAULT));
+ HDF5_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &ioffsetdenom[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ ivect const ioffset = ((bbox.lower() % bbox.stride()) + bbox.stride()) % bbox.stride();
+ HDF5_ERROR (attr = H5Acreate (dataset, "ioffset", H5T_NATIVE_INT,
+ dataspace, H5P_DEFAULT));
+ HDF5_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &ioffset[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ ivect const iorigin = (bbox.lower() - ioffset) / bbox.stride();
HDF5_ERROR (attr = H5Acreate (dataset, "iorigin", H5T_NATIVE_INT,
dataspace, H5P_DEFAULT));
HDF5_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &iorigin[0]));
diff --git a/Carpet/CarpetIOHDF5/src/OutputSlice.cc b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
index a87fe0a79..90e9539bc 100644
--- a/Carpet/CarpetIOHDF5/src/OutputSlice.cc
+++ b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
@@ -1381,6 +1381,8 @@ namespace CarpetIOHDF5 {
slice_start, NULL, slice_count, NULL));
vector<int> iorigin(rank, 0);
+ vector<int> ioffset(rank, 0);
+ vector<int> ioffsetdenom(rank, 1);
vector<double> delta(rank, 0), origin(rank, 0);
vector<int> bbox(2*rank, 0), nghostzones(rank, 0);
for (int d = 0; d < outdim; d++) {
@@ -1392,7 +1394,10 @@ namespace CarpetIOHDF5 {
delta[d] = (coord_upper[dirs[d]] - coord_lower[dirs[d]]) /
(gfext.upper()[dirs[d]] - gfext.lower()[dirs[d]]) * gfext.stride()[dirs[d]];
origin[d] += (org1[dirs[d]] - gfext.lower()[dirs[d]]) * delta[d];
- iorigin[d] /= gfext.stride()[dirs[d]];
+ ioffsetdenom[d] = gfext.stride()[dirs[d]];
+ ioffset[d] = (iorigin[d] % gfext.stride()[dirs[d]] + gfext.stride()[dirs[d]]) % gfext.stride()[dirs[d]];
+ assert ((iorigin[d] - ioffset[d]) % gfext.stride()[dirs[d]] == 0);
+ iorigin[d] = (iorigin[d] - ioffset[d]) / gfext.stride()[dirs[d]];
}
}
// store cctk_bbox and cctk_nghostzones (for grid arrays only)
@@ -1432,7 +1437,7 @@ namespace CarpetIOHDF5 {
H5P_DEFAULT, gfdatas[n]->storage()));
error_count +=
AddSliceAttributes (cctkGH, fullname, rl, ml, m, tl, origin, delta,
- iorigin, bbox, nghostzones, dataset);
+ iorigin, ioffset, ioffsetdenom, bbox, nghostzones, dataset);
HDF5_ERROR(H5Dclose (dataset));
free (fullname);
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-29 02:13:53 +0000