Hi everyone:
I met trouble when I tried to plot derived vorticity field in yt.
The dataset is written in AMRex form (multiple layers).
However, it will call Runtimeerror raised by "in _fill_fields" in construction_data_containers.py.
I will be appreciate if anyone can give me some suggestions!
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Here is python command in brief (ds is dataset, u,v are velocity component in x, y direction, vor_z is Vorticity in z direction):
for ds in ts.piter():
ds.periodicity=(False,False,False)
u_gradient = ds.add_gradient_fields(("boxlib","u_mixt"))
v_gradient = ds.add_gradient_fields(("boxlib","v_mixt"))
derived_fields = [ # field name, units, displayname
('vort_z', '1 / cm', 'Vorticity in z direction'),
]
for name, unitstr, dispname in derived_fields:
ds.add_field(
('boxlib', name),
units = unitstr,
function = eval(name + '_func'),
sampling_type = 'cell',
display_name = dispname
)
chang =0.112
kuan =0.056
slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([0.48,0.028,0.01],'cm'))
slc.save()
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Here is the error info:
yt : [ERROR ] RuntimeError:
1005 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
1006 File "vorfield.py", line 90, in <module>
1007 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([0.46,0.028,0.01],'cm'))
1008 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot
1009 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
1010 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__
1011 slc.get_data(fields)
1012 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data
1013 self._generate_fields(fields_to_generate)
1014 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields
1015 fd = self._generate_field(field)
1016 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field
1017 tr = self._generate_fluid_field(field)
1018 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field
1019 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
1020 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid
1021 gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz],
1022 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__
1023 self.get_data(f)
1024 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data
1025 if len(fill) > 0: self._fill_fields(fill)
1026 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1060, in _fill_fields
1027 raise RuntimeError
best wishes,
He Yifeng