[yt-users] Inspecting gradient of a field at boundary

[tazkera haque]

Hi people,

I am trying to define curl of a vector field in yt, but first I needed to
see if correct derivatives are taken at the boundary. I am starting with a
mock data set and followed yt tutorial:

import yt
from yt import YTArray
import numpy as np

posx = np.linspace(-1.0,1.0,12)
posy = np.linspace(-1.0,1.0,12)
posz = np.linspace(-1.0,1.0,12)

X, Y, Z = np.meshgrid(posx, posy, posz, indexing='ij') # From gradient
output, yt seems to use ij indexing

psi = X

data_dict = {"psi":(psi,'kg/cm**3'),
            "number_of_particles":12,
            "particle_position_x":(posx, 'kg/cm**3'),
            "particle_position_y":(posy, 'kg/cm**3'),
            "particle_position_z":(posz, 'kg/cm**3')}

bbox = np.array([[-1.0, 1.0], [-1.0, 1.0], [-1.0, 1.0]])

y  = yt.load_uniform_grid(data_dict,domain_dimensions=(12,12,12),bbox=bbox)

grad_fields = y.add_gradient_fields(("stream","psi"))

ad = y.all_data()

print( ad["psi_gradient_x"] )
print( ad["psi_gradient_y"] )
print( ad["psi_gradient_z"] )

Output:
yt : [INFO     ] 2017-05-17 19:40:16,410 Parameters: current_time
   = 0.0
yt : [INFO     ] 2017-05-17 19:40:16,410 Parameters: domain_dimensions
    = [12 12 12]
yt : [INFO     ] 2017-05-17 19:40:16,411 Parameters: domain_left_edge
   = [-1. -1. -1.]
yt : [INFO     ] 2017-05-17 19:40:16,411 Parameters: domain_right_edge
    = [ 1.  1.  1.]
yt : [INFO     ] 2017-05-17 19:40:16,412 Parameters:
cosmological_simulation   = 0.0
[-5.45454545 -5.45454545 -5.45454545 ..., -5.45454545 -5.45454545
 -5.45454545] kg/cm**4
[ 0.  0.  0. ...,  0.  0.  0.] kg/cm**4
[ 0.  0.  0. ...,  0.  0.  0.] kg/cm**4


Now my question is, since psi(x,y,z) = x, the gradient should be
(1,0,0)...and it is everywhere except the boundaries of the box. Can you
please explain to me what is going wrong here? I don't
   think YT is interpreting the bbox and grid points as I am.

Best
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