Merge pull request #5155 from mabruzzo/cholla-mu-fix

BUG: Better behavior when Cholla doesn't write "mu" attribute

Author: chrishavlin

yt/frontends/cholla/data_structures.py

@@ -8,6 +8,7 @@
 from yt.funcs import setdefaultattr
 from yt.geometry.api import Geometry
 from yt.geometry.grid_geometry_handler import GridIndex
+from yt.utilities.logger import ytLogger as mylog
 from yt.utilities.on_demand_imports import _h5py as h5py
 
 from .fields import ChollaFieldInfo
@@ -111,7 +112,19 @@ def _parse_parameter_file(self):
             self.current_time = attrs["t"][:]
             self._periodicity = tuple(attrs.get("periodicity", (False, False, False)))
             self.gamma = attrs.get("gamma", 5.0 / 3.0)
-            self.mu = attrs.get("mu", 1.0)
+            if (self.default_species_fields is not None) and "mu" in attrs:
+                raise ValueError(
+                    'default_species_fields must be None when "mu" is an hdf5 attribute'
+                )
+            elif "mu" in attrs:
+                self.mu = attrs["mu"]
+            elif self.default_species_fields is None:
+                # other yt-machinery can't handle ds.mu == None, so we simply
+                # avoid defining the mu attribute if we don't know its value
+                mylog.info(
+                    'add the "mu" hdf5 attribute OR use the default_species_fields kwarg '
+                    "to compute temperature"
+                )
             self.refine_by = 1
 
             # If header specifies code units, default to those (in CGS)

yt/frontends/cholla/fields.py

@@ -87,21 +87,23 @@ def _specific_total_energy(field, data):
         )
 
         # Add temperature field
-        def _temperature(field, data):
-            return (
-                data.ds.mu
-                * data["gas", "pressure"]
-                / data["gas", "density"]
-                * mh
-                / kboltz
-            )
+        if hasattr(self.ds, "mu"):
+
+            def _temperature(field, data):
+                return (
+                    data.ds.mu
+                    * data["gas", "pressure"]
+                    / data["gas", "density"]
+                    * mh
+                    / kboltz
+                )
 
-        self.add_field(
-            ("gas", "temperature"),
-            sampling_type="cell",
-            function=_temperature,
-            units=unit_system["temperature"],
-        )
+            self.add_field(
+                ("gas", "temperature"),
+                sampling_type="cell",
+                function=_temperature,
+                units=unit_system["temperature"],
+            )
 
         # Add color field if present (scalar0 / density)
         if ("cholla", "scalar0") in self.field_list: