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Fix small bugs/edge cases in the parthenon frontend #5276

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Merged
chrishavlin merged 10 commits into from
Oct 15, 2025
Merged

Fix small bugs/edge cases in the parthenon frontend #5276

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dbd582d
update yt to work with riot. Still need to check on diffusion groups
jonahm-LANL Aug 26, 2025
93e0160
Merge remote-tracking branch 'upstream/main' into jmm/parthenon-front…
pgrete Sep 5, 2025
62a5289
Add RIOT skeleton
pgrete Sep 5, 2025
ad28ef0
Fix typi
pgrete Sep 5, 2025
f7d27e7
added more concrete tests
jonahm-LANL Sep 13, 2025
fd336c3
more clean
jonahm-LANL Sep 13, 2025
d7453ae
Update yt/frontends/parthenon/data_structures.py
Yurlungur Oct 9, 2025
2b3b9b3
remove reference to axis order in init
jonahm-LANL Oct 10, 2025
2503878
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 13, 2025
a39fbd5
Merge remote-tracking branch 'upstream/main' into parthenon_merge
chrishavlin Oct 15, 2025
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10 changes: 0 additions & 10 deletions yt/frontends/parthenon/data_structures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,10 +53,6 @@ def _setup_dx(self):
id = self.id - self._id_offset
LE, RE = self.index.grid_left_edge[id, :], self.index.grid_right_edge[id, :]
self.dds = self.ds.arr((RE - LE) / self.ActiveDimensions, "code_length")
if self.ds.dimensionality < 2:
self.dds[1] = 1.0
if self.ds.dimensionality < 3:
self.dds[2] = 1.0
self.field_data["dx"], self.field_data["dy"], self.field_data["dz"] = self.dds

def retrieve_ghost_zones(self, n_zones, fields, all_levels=False, smoothed=False):
Expand Down Expand Up @@ -164,19 +160,13 @@ def __init__(

self.geometry = _geom_map[self._handle["Info"].attrs["Coordinates"]]

if self.geometry is Geometry.CYLINDRICAL:
axis_order = ("r", "theta", "z")
else:
axis_order = None

Dataset.__init__(
self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system,
default_species_fields=default_species_fields,
axis_order=axis_order,
)
if storage_filename is None:
storage_filename = self.basename + ".yt"
Expand Down
10 changes: 8 additions & 2 deletions yt/frontends/parthenon/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,10 @@ def _read_fluid_selection(self, chunks, selector, fields, size):
for gs in grid_sequences(chunk.objs):
start = gs[0].id - gs[0]._id_offset
end = gs[-1].id - gs[-1]._id_offset + 1
data = ds[start:end, fdi, :, :, :].transpose()
if len(ds.shape) == 4:
data = ds[start:end, :, :, :].transpose()
else:
data = ds[start:end, fdi, :, :, :].transpose()
Comment on lines +55 to +58
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@Yurlungur Yurlungur Aug 29, 2025

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Parthenon's python reader can always split a variable into a flat index space, so I think this is now generic.

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@pgrete pgrete Sep 2, 2025

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I'm not sure I understand this change. What's exactly happening here?
a) the Parthenon python reader is not used in yt
b) a flattened index space (from a vector or tensor variable) would always carry the fdi index, doesn't it?

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@Yurlungur Yurlungur Sep 2, 2025

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In riot's current format scalar fields are only 4D with the leading index the block. AthenaPK doesn't see this because it has a prim vector, but riot and phoebus do. That's what's this change is. I didn't modify the piece with prim vector, just special case scalars.

for i, g in enumerate(gs):
ind += g.select(selector, data[..., i], rv[field], ind)
last_dname = dname
Expand All @@ -72,7 +75,10 @@ def _read_chunk_data(self, chunk, fields):
for gs in grid_sequences(chunk.objs):
start = gs[0].id - gs[0]._id_offset
end = gs[-1].id - gs[-1]._id_offset + 1
data = ds[start:end, fdi, :, :, :].transpose()
if len(ds.shape) == 4:
data = ds[start:end, :, :, :].transpose()
else:
data = ds[start:end, fdi, :, :, :].transpose()
for i, g in enumerate(gs):
rv[g.id][field] = np.asarray(data[..., i], "=f8")
return rv
22 changes: 22 additions & 0 deletions yt/frontends/parthenon/tests/test_outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,3 +179,25 @@ def test_load_cylindrical():
# Check that the domain edges match r in [0.5,2.0], theta in [0, 2pi]
assert_equal(ds.domain_left_edge.in_units("code_length").v[:2], (0.5, 0))
assert_equal(ds.domain_right_edge.in_units("code_length").v[:2], (2.0, 2 * np.pi))


# Sedov blast wave with curvlinear coords run with RIOT
riot_sedov_curvlinear = "riot_sedov_curvlinear/sedov.out1.final.phdf"


@requires_file(riot_sedov_curvlinear)
def test_load_riot_curvilinear():
# Load a cylindrical dataset of a full disk
ds = data_dir_load(riot_sedov_curvlinear)

assert ("parthenon", "c.c.bulk.pressure") in ds.field_list

ad = ds.all_data()
dth = ad["index", "dtheta"]
vol = ad["index", "cell_volume"]
rho = ad["parthenon", "c.c.bulk.rho"]

assert np.all(np.abs(dth - 2 * np.pi) <= 1e-12)

total_mass = (rho * vol).sum()
assert np.all(np.abs(total_mass.value - 0.169646) <= 1e-8)
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