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Add support for Enzo-E simulations with 0 ghost zones #4932

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merged 2 commits into from
Jul 16, 2024
Merged

Add support for Enzo-E simulations with 0 ghost zones #4932

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6ee41e8
add support for enzo-e sims without any ghost zones.
mabruzzo Jun 22, 2024
16238b7
addressing suggestion from @neutrinoceros
mabruzzo Jun 23, 2024
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6 changes: 5 additions & 1 deletion yt/frontends/enzo_e/data_structures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -408,7 +408,11 @@ def _parse_parameter_file(self):
self.parameters["current_cycle"] = ablock.attrs["cycle"][0]
gsi = ablock.attrs["enzo_GridStartIndex"]
gei = ablock.attrs["enzo_GridEndIndex"]
self.ghost_zones = gsi[0]
assert len(gsi) == len(gei) == 3 # sanity check
# Enzo-E technically allows each axis to have different ghost zone
# depths (this feature is not really used in practice)
self.ghost_zones = gsi
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although technically not backward compatible, I don't expect anyone to rely on the old behavior so I'm tempted to just let this change in.

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I definitely agree, especially because pool of enzo-e users is currently very small. (At most, there are maybe 5 people who regularly use the yt-frontend right now)

But, let me know if you would prefer I change it (and whether there is an obvious preferred way to do it)

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I think it's fine as is. I'll just give it a couple weeks before merging in case anyone objects.

assert (self.ghost_zones[self.dimensionality :] == 0).all() # sanity check
self.root_block_dimensions = root_blocks
self.active_grid_dimensions = gei - gsi + 1
self.grid_dimensions = ablock.attrs["enzo_GridDimension"]
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15 changes: 12 additions & 3 deletions yt/frontends/enzo_e/io.py
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Expand Up @@ -14,8 +14,17 @@ class EnzoEIOHandler(BaseIOHandler):

def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._base = self.ds.dimensionality * (
slice(self.ds.ghost_zones, -self.ds.ghost_zones),

# precompute the indexing specifying each field's active zone
# -> this assumes that each field in Enzo-E shares the same number of
# ghost-zones. Technically, Enzo-E allows each field to have a
# different number of ghost zones (but this feature isn't currently
# used & it currently doesn't record this information)
# -> our usage of a negative stop value ensures compatability with
# both cell-centered and face-centered fields
self._activezone_idx = tuple(
slice(num_zones, -num_zones) if num_zones > 0 else slice(None)
for num_zones in self.ds.ghost_zones[: self.ds.dimensionality]
)

# Determine if particle masses are actually masses or densities.
Expand Down Expand Up @@ -186,7 +195,7 @@ def _read_obj_field(self, obj, field, fid_data):
dg.read(h5py.h5s.ALL, h5py.h5s.ALL, rdata)
if close:
fid.close()
data = rdata[self._base].T
data = rdata[self._activezone_idx].T
if self.ds.dimensionality < 3:
nshape = data.shape + (1,) * (3 - self.ds.dimensionality)
data = np.reshape(data, nshape)
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