Hi all, I'm using yt to analize ZEUS simulations. I have been able to remap all the native fields on a custom AMR grid that I created, and I load the data in the GDF format. I'm very happy with this, but when I try to calculate the Xray emissivity using this little script here: import yt from yt.analysis_modules.spectral_integrator.api import \ add_xray_emissivity_field ds=yt.load('GDFhdfaa.0000073.hdf5') xray_fields = add_xray_emissivity_field(ds, 0.2, 8.0, with_metals=False, constant_metallicity=0.5) plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') I get the error: Traceback (most recent call last): File "./xray.py", line 11, in <module> plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/visualization/plot_window.py", line 1495, in __init__ max_level=max_level) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 263, in __init__ self.get_data(field) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 337, in get_data self._handle_chunk(chunk, fields, tree) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 437, in _handle_chunk d = chunk[field] * dl File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1295, in get_data self._generate_fields(fields_to_generate) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1346, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'H_number_density')' returned data with units 'dimensionless/g' but was defined with units 'cm**-3'. I tried to check the GDF frontend, but I'm able to understand if the error is there or somewhere else... You can find a very light dataset in the GDF format in attachment, if you want ot reproduce the error. You need to download both files, since in the GDF file there are some hard links to the amr2 file (still an hdf5 file). I tried both the stable and the developer version of yt, and the error is the same. Any ideas? I really think that my GDF file is correct, since I'm able to slice and project all the native fields (density, temperature, velocities...). Thanks, Andrea
Hi Andrea, I am not an expert on the GDF format, but the problem seems to be that your fields are not getting the appropriate units defined for them. For example, you can see this by doing: ds=yt.load('GDFhdfaa.0000073.hdf5') print (ds.r[("gas", "density")]) You'll notice that they come up as dimensionless. I believe you can correct this by adding an attribute called "field_units" to each dataset with a string that indicates the units of the data. For example, with density, you would have "g/cm**3". Britton On Sun, Nov 20, 2016 at 4:19 AM, Andrea Negri <negri.andre@gmail.com> wrote:
Hi all,
I'm using yt to analize ZEUS simulations. I have been able to remap all the native fields on a custom AMR grid that I created, and I load the data in the GDF format.
I'm very happy with this, but when I try to calculate the Xray emissivity using this little script here:
import yt from yt.analysis_modules.spectral_integrator.api import \ add_xray_emissivity_field
ds=yt.load('GDFhdfaa.0000073.hdf5') xray_fields = add_xray_emissivity_field(ds, 0.2, 8.0, with_metals=False, constant_metallicity=0.5) plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV')
I get the error:
Traceback (most recent call last): File "./xray.py", line 11, in <module> plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/ visualization/plot_window.py", line 1495, in __init__ max_level=max_level) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/construction_data_containers.py", line 263, in __init__ self.get_data(field) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/construction_data_containers.py", line 337, in get_data self._handle_chunk(chunk, fields, tree) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/construction_data_containers.py", line 437, in _handle_chunk d = chunk[field] * dl File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/data_containers.py", line 1295, in get_data self._generate_fields(fields_to_generate) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_ objects/data_containers.py", line 1346, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'H_number_density')' returned data with units 'dimensionless/g' but was defined with units 'cm**-3'.
I tried to check the GDF frontend, but I'm able to understand if the error is there or somewhere else... You can find a very light dataset in the GDF format in attachment, if you want ot reproduce the error. You need to download both files, since in the GDF file there are some hard links to the amr2 file (still an hdf5 file). I tried both the stable and the developer version of yt, and the error is the same.
Any ideas? I really think that my GDF file is correct, since I'm able to slice and project all the native fields (density, temperature, velocities...).
Thanks, Andrea
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Hi Britton, thanks, this was the problem. The unit was already in the file, but I named the attribute "field_unit" instead of "field_units". Now it works and the numbers make sense. Cheers, Andrea On 20 November 2016 at 19:04, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Andrea,
I am not an expert on the GDF format, but the problem seems to be that your fields are not getting the appropriate units defined for them. For example, you can see this by doing: ds=yt.load('GDFhdfaa.0000073.hdf5') print (ds.r[("gas", "density")])
You'll notice that they come up as dimensionless. I believe you can correct this by adding an attribute called "field_units" to each dataset with a string that indicates the units of the data. For example, with density, you would have "g/cm**3".
Britton
On Sun, Nov 20, 2016 at 4:19 AM, Andrea Negri <negri.andre@gmail.com> wrote:
Hi all,
I'm using yt to analize ZEUS simulations. I have been able to remap all the native fields on a custom AMR grid that I created, and I load the data in the GDF format.
I'm very happy with this, but when I try to calculate the Xray emissivity using this little script here:
import yt from yt.analysis_modules.spectral_integrator.api import \ add_xray_emissivity_field
ds=yt.load('GDFhdfaa.0000073.hdf5') xray_fields = add_xray_emissivity_field(ds, 0.2, 8.0, with_metals=False, constant_metallicity=0.5) plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV')
I get the error:
Traceback (most recent call last): File "./xray.py", line 11, in <module> plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/visualization/plot_window.py", line 1495, in __init__ max_level=max_level) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 263, in __init__ self.get_data(field) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 337, in get_data self._handle_chunk(chunk, fields, tree) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 437, in _handle_chunk d = chunk[field] * dl File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1295, in get_data self._generate_fields(fields_to_generate) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1346, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'H_number_density')' returned data with units 'dimensionless/g' but was defined with units 'cm**-3'.
I tried to check the GDF frontend, but I'm able to understand if the error is there or somewhere else... You can find a very light dataset in the GDF format in attachment, if you want ot reproduce the error. You need to download both files, since in the GDF file there are some hard links to the amr2 file (still an hdf5 file). I tried both the stable and the developer version of yt, and the error is the same.
Any ideas? I really think that my GDF file is correct, since I'm able to slice and project all the native fields (density, temperature, velocities...).
Thanks, Andrea
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participants (2)
-
Andrea Negri -
Britton Smith