[yt-users] Re: Key error using gradient fields with Enzo

Hi Sam, The call to SlicePlot should look like this: SlicePlot(ds, “z”, 'velocity_x_gradient_x') Note how I’m passing a string field name, not the field array data. Nathan On Mon, Jan 29, 2018 at 5:23 AM Sam Patrick wrote:

Hi,

thanks for the advice on data objects. It appears that assigning the derived field to a variable no longer creates a problem anymore. However, I'm still having trouble plotting the field. When I try to plot the field by using the data object as the first argument of SlicePlot, such as in the construction below, I get an error stating that this isn't possible since the object lacks inbuilt coordinates:

import yt from yt.units import pc, Msun, Myr from yt.units.yt_array import YTArray from yt import derived_field import numpy as np

yt.enable_parallelism()

ds = yt.load("DD0045/output_0045")

val, loc = ds.find_max('density')

ds.periodicity = (True, True, True)

ds.add_gradient_fields(('gas', 'velocity_x'))

right_edge = loc - YTArray(np.full((3), 6.0), 'pc') left_edge = loc + YTArray(np.full((3), 6.0), 'pc') box = ds.region(loc, right_edge, left_edge)

grad_x = box['velocity_x_gradient_x']

plt = yt.SlicePlot(box, 'z', grad_x, center= loc, width= (6.0, 'pc'))

plt.save("plot.png")

File "plot_curl.py", line 54, in <module> plt = yt.SlicePlot(box, 'z', grad_x, center= loc, width= (6.0, 'pc')) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1897, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1240, in __init__ axis = fix_axis(axis, ds) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/funcs.py", line 708, in fix_axis return ds.coordinates.axis_id.get(axis, axis) P009 yt : [ERROR ] 2018-01-29 10:58:59,487 AttributeError: 'YTRegion' object has no attribute 'coordinates'

When I instead attempt to use the dataset itself as the first argument of SlicePlot, by replacing the penultimate line of code with:

plt = yt.SlicePlot(ds, 'z', grad_x, center= loc, width= (6.0, 'pc'))

I get the following error message:

File "plot_curl.py", line 49, in <module> plt = yt.SlicePlot(ds, 'z', curl_mag, center= loc, width= (6.0, 'pc')) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1897, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1255, in __init__ slc.get_data(fields) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1123, in get_data for field in self._determine_fields(fields): File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 993, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 638, in _get_field_info if field in self.field_info: File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/fields/field_info_container.py", line 337, in __contains__ if dict.__contains__(self, key): return True P011 yt : [ERROR ] 2018-01-26 14:09:47,834 TypeError: unhashable type: 'YTArray'

Is there a possible solution to this?

Many thanks, Sam

On 25/01/18 14:32, Nathan Goldbaum wrote:

Hi Sam,

A construction like this:

ds[key]

Is a way of getting runtime parameters from the dataset, not accessing a field. The reason your script is failing is that “velocity_x_gradient_x” is a field, not a runtime parameter, so the key error you get is appropriate.

If you want to access field values, you need to create a data object first:

ad = ds.all_data() ad[“velocity_x_gradient_x”]

There are a number of data objects in yt, see:

http://yt-project.org/doc/analyzing/objects.html

Finally, yt 3.3.1 is somewhat out of date, the latest version is yt 3.4.0. You likely want to upgrade if you are able to since 3.4.0 includes a number of fixes for issues in the 3.3.x series.

Best,

Nathan

On Thu, Jan 25, 2018 at 8:25 AM Sam Patrick wrote:

...

Hello all,

I am rather new to yt and have recently tried using the gradient fields functionality. I'm attempting to write a script which involves basic calculations with the gradient of the velocity field, however I keep coming across the same error when assigning the gradient field to a variable.

My current version of yt is 3.3.1 and my version of Python is 2.7.12. The data dumps I'm reading from were produced by an Enzo cosmology simulation (version 2.5).

The following code is a simplified version of the script which runs successfully and outputs a slice plot of the velocity gradient:

import yt from yt import derived_field

yt.enable_parallelism()

ds = yt.load("DD0045/output_0045") val, loc = ds.find_max('density')

ds.periodicity = (True, True, True)

ds.add_gradient_fields(('gas', 'velocity_x'))

#grad_x = ds['velocity_x_gradient_x']

plt = yt.SlicePlot(ds, 'z', 'velocity_x_gradient_x', center= loc, width= (6.0, 'pc')

plt.save("plot.png")

However, when I try to assign this gradient field to a variable by removing the comment and adding the line "grad_x = ds['velocity_x_gradient_x']" and plotting this instead I come across the following error:

File

"/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 352, in __getitem__ return self.parameters[key] P015 yt : [ERROR ] 2018-01-25 10:49:00,443 KeyError: 'velocity_x_gradient_x'

I am unsure what I am doing wrong here. Any help will be very much appreciated.

Thanks, Sam Patrick

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