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Merge pull request #450 from unoebauer/zero_volume_fix
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Checking for zero-volume cells: Fixes issue #79
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@ssim
ssim committed Dec 10, 2015
2 parents f07ab83 + 7ff44f4 commit 86a7d95
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Showing 3 changed files with 99 additions and 5 deletions.
21 changes: 18 additions & 3 deletions tardis/io/model_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def read_density_file(density_filename, density_filetype, time_explosion,
raise ConfigurationError('v_inner_boundary > v_outer_boundary '
'({0:s} > {1:s}). unphysical!'.format(
v_inner_boundary, v_outer_boundary))

if (not np.isclose(v_inner_boundary, 0.0 * u.km / u.s,
atol=1e-8 * u.km / u.s)
and v_inner_boundary > v_inner[0]):
Expand All @@ -52,6 +52,11 @@ def read_density_file(density_filename, density_filetype, time_explosion,
raise ConfigurationError('Inner boundary selected outside of model')

inner_boundary_index = v_inner.searchsorted(v_inner_boundary) - 1
# check for zero volume of designated first cell
if np.isclose(v_inner_boundary, v_inner[inner_boundary_index + 1],
atol=1e-8 * u.km / u.s) and (v_inner_boundary <=
v_inner[inner_boundary_index + 1]):
inner_boundary_index += 1

else:
inner_boundary_index = None
Expand All @@ -66,7 +71,7 @@ def read_density_file(density_filename, density_filetype, time_explosion,
v_outer_boundary = v_outer[-1]
logger.warning("v_outer_boundary requested too large for readin file. Boundary shifted to match file.")


v_inner = v_inner[inner_boundary_index:outer_boundary_index]
v_inner[0] = v_inner_boundary

Expand All @@ -75,6 +80,16 @@ def read_density_file(density_filename, density_filetype, time_explosion,

mean_densities = mean_densities[inner_boundary_index:outer_boundary_index]

invalid_volume_mask = (v_outer - v_inner) <= 0
if invalid_volume_mask.sum() > 0:
message = "\n".join(["cell {0:d}: v_inner {1:s}, v_outer "
"{2:s}".format(i, v_inner_i, v_outer_i) for i,
v_inner_i, v_outer_i in
zip(np.arange(len(v_outer))[invalid_volume_mask],
v_inner[invalid_volume_mask],
v_outer[invalid_volume_mask])])
raise ConfigurationError("Invalid volume of following cell(s):\n"
"{:s}".format(message))

return (v_inner, v_outer, mean_densities,
inner_boundary_index, outer_boundary_index)
Expand Down Expand Up @@ -107,7 +122,7 @@ def read_abundances_file(abundance_filename, abundance_filetype,

index, abundances = file_parsers[abundance_filetype](abundance_filename)
if outer_boundary_index is not None:
outer_boundary_index_m1 = outer_boundary_index - 1
outer_boundary_index_m1 = outer_boundary_index - 1
else:
outer_boundary_index_m1 = None
index = index[inner_boundary_index:outer_boundary_index]
Expand Down
72 changes: 72 additions & 0 deletions tardis/io/tests/data/invalid_artis_model.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
70
0.00114661
1 1.259375e+03 -5.449497e-05 9.969498e-01 9.787696e-01 6.973734e-06 5.052319e-06 6.168110e-07
2 1.574219e+03 3.013383e-04 9.969307e-01 9.788986e-01 6.845718e-06 5.013408e-06 6.140697e-07
3 1.889063e+03 -1.982630e-02 9.968976e-01 9.789760e-01 6.720018e-06 4.915389e-06 6.130545e-07
4 2.203907e+03 -4.429480e-02 9.968509e-01 9.790147e-01 6.608687e-06 4.839975e-06 6.060005e-07
5 2.518750e+03 -5.767948e-02 9.967775e-01 9.789697e-01 6.505750e-06 4.727071e-06 6.067441e-07
6 2.833594e+03 -7.370731e-02 9.966485e-01 9.787804e-01 6.395329e-06 4.580685e-06 6.268937e-07
7 3.148438e+03 -1.013941e-01 9.964382e-01 9.783643e-01 6.259683e-06 4.443940e-06 6.797306e-07
8 3.463282e+03 -1.223770e-01 9.961101e-01 9.776204e-01 6.090588e-06 4.411024e-06 7.830217e-07
9 3.778126e+03 -1.441526e-01 9.956658e-01 9.765878e-01 5.894967e-06 4.667291e-06 9.375288e-07
10 4.092969e+03 -1.710595e-01 9.951726e-01 9.754603e-01 5.696173e-06 5.264160e-06 1.113761e-06
11 4.407813e+03 -1.921165e-01 9.946904e-01 9.743882e-01 5.505227e-06 6.087066e-06 1.275082e-06
12 4.722657e+03 -2.190449e-01 9.942578e-01 9.734612e-01 5.318957e-06 6.965121e-06 1.406783e-06
13 5.037501e+03 -2.503739e-01 9.938884e-01 9.727036e-01 5.138882e-06 7.761285e-06 1.503072e-06
14 5.352345e+03 -2.796168e-01 9.936060e-01 9.721567e-01 4.966839e-06 8.340429e-06 1.549395e-06
15 5.667188e+03 -3.105920e-01 9.934865e-01 9.719984e-01 4.797945e-06 8.454966e-06 1.503797e-06
16 5.667188e+03 -3.413327e-01 9.937069e-01 9.726593e-01 4.642989e-06 7.660500e-06 1.276586e-06
17 6.296876e+03 -3.751951e-01 9.946118e-01 9.750052e-01 4.504424e-06 5.799124e-06 7.959853e-07
18 6.611720e+03 -4.087162e-01 9.968127e-01 9.809170e-01 4.377842e-06 1.154036e-05 2.120706e-07
19 6.926563e+03 -4.452069e-01 9.993206e-01 9.838294e-01 4.787479e-06 7.603537e-03 1.054282e-04
20 7.241407e+03 -4.782779e-01 9.934882e-01 9.623342e-01 7.808212e-06 2.142014e-02 4.893291e-04
21 7.556251e+03 -5.144547e-01 9.801450e-01 9.390609e-01 7.891220e-06 2.628785e-02 7.470313e-04
22 7.871095e+03 -5.506459e-01 9.570934e-01 9.065100e-01 7.418816e-06 2.935965e-02 9.643208e-04
23 8.185939e+03 -5.838073e-01 9.166762e-01 8.554363e-01 6.813265e-06 3.148066e-02 1.174981e-03
24 8.500782e+03 -6.187967e-01 8.444416e-01 7.711242e-01 6.021313e-06 3.228287e-02 1.373482e-03
25 8.815626e+03 -6.478082e-01 7.205625e-01 6.360884e-01 4.926903e-06 3.042671e-02 1.489358e-03
26 9.130470e+03 -6.772585e-01 5.522046e-01 4.633726e-01 3.580056e-06 2.523080e-02 1.421018e-03
27 9.445314e+03 -7.025316e-01 3.798727e-01 2.967333e-01 2.290327e-06 1.821502e-02 1.174456e-03
28 9.360158e+03 -7.393099e-01 2.434208e-01 1.729650e-01 1.321915e-06 1.181660e-02 8.653664e-04
29 1.007500e+04 -7.769093e-01 1.593954e-01 1.020666e-01 7.627219e-07 7.574566e-03 6.170831e-04
30 1.038985e+04 -8.221853e-01 1.137370e-01 6.635599e-02 4.797101e-07 5.202758e-03 4.581936e-04
31 1.070469e+04 -8.745196e-01 8.964338e-02 4.874161e-02 3.390994e-07 3.947096e-03 3.661284e-04
32 1.101953e+04 -9.296468e-01 7.628418e-02 3.940266e-02 2.635893e-07 3.241346e-03 3.114475e-04
33 1.133438e+04 -9.903432e-01 6.722356e-02 3.232460e-02 2.087902e-07 2.646639e-03 2.642194e-04
34 1.164922e+04 -1.044582e+00 5.923151e-02 2.301299e-02 1.443657e-07 1.793031e-03 1.973346e-04
35 1.196406e+04 -1.107672e+00 5.226578e-02 1.259155e-02 7.754713e-08 8.991098e-04 1.268152e-04
36 1.227891e+04 -1.166106e+00 4.718720e-02 5.081296e-03 3.147591e-08 3.251325e-04 7.181194e-05
37 1.259375e+04 -1.224244e+00 3.832284e-02 1.308496e-03 1.028649e-08 6.508490e-05 2.581188e-05
38 1.290860e+04 -1.278808e+00 2.325070e-02 1.854372e-04 8.404720e-09 5.333218e-06 3.988807e-06
39 1.322344e+04 -1.319016e+00 9.104333e-03 1.132432e-05 2.479127e-09 3.431589e-07 4.391149e-07
40 1.353828e+04 -1.339697e+00 9.852053e-04 1.299599e-07 7.783476e-11 1.265313e-08 2.057230e-08
41 1.385313e+04 -1.350281e+00 3.185364e-05 9.492013e-10 1.632555e-12 1.190779e-10 2.088784e-10
42 1.416797e+04 -1.366863e+00 1.474822e-05 2.220123e-10 5.309134e-13 4.447397e-11 7.551816e-11
43 1.448281e+04 -1.408773e+00 8.973184e-06 8.011853e-11 2.082280e-13 3.914228e-11 5.869264e-11
44 1.479766e+04 -1.484229e+00 6.154459e-06 2.021216e-11 5.137364e-14 2.829258e-11 6.464542e-11
45 1.511250e+04 -1.576636e+00 5.280028e-06 6.933790e-12 1.465119e-14 1.530388e-11 6.442062e-11
46 1.542735e+04 -1.673018e+00 5.236783e-06 3.220037e-12 6.011255e-15 8.828028e-12 6.008495e-11
47 1.574219e+04 -1.779685e+00 5.475689e-06 1.656054e-12 3.293192e-15 5.715768e-12 5.706669e-11
48 1.605703e+04 -1.876238e+00 5.822625e-06 8.090158e-13 1.990751e-15 3.956454e-12 5.687796e-11
49 1.637188e+04 -1.990179e+00 6.233115e-06 4.442047e-13 1.473151e-15 3.072241e-12 5.915856e-11
50 1.668672e+04 -2.082134e+00 6.693559e-06 2.602742e-13 1.196462e-15 2.628631e-12 6.268807e-11
51 1.700156e+04 -2.189603e+00 7.080294e-06 1.937764e-13 1.302169e-15 2.424756e-12 6.402162e-11
52 1.731641e+04 -2.251445e+00 7.367846e-06 1.874260e-13 2.002987e-15 2.292432e-12 6.198017e-11
53 1.763125e+04 -2.336874e+00 7.487331e-06 2.089537e-13 3.862363e-15 2.145276e-12 5.615828e-11
54 1.794610e+04 -2.413082e+00 7.481771e-06 2.284368e-13 7.610089e-15 1.892516e-12 4.869019e-11
55 1.826094e+04 -2.525231e+00 7.307651e-06 2.426003e-13 1.494172e-14 1.604724e-12 4.093251e-11
56 1.857578e+04 -2.598198e+00 6.904268e-06 2.392776e-13 2.741366e-14 1.286481e-12 3.355300e-11
57 1.889063e+04 -2.582957e+00 6.180129e-06 2.125336e-13 4.712860e-14 9.528658e-13 2.601973e-11
58 1.920547e+04 -2.732132e+00 5.130247e-06 1.782245e-13 7.413013e-14 6.634504e-13 1.942738e-11
59 1.952032e+04 -2.787764e+00 4.160961e-06 1.395227e-13 9.871988e-14 4.585879e-13 1.521031e-11
60 1.983516e+04 -2.847531e+00 3.126174e-06 9.689468e-14 1.121511e-13 2.803738e-13 1.103460e-11
61 2.015000e+04 -2.861318e+00 2.165275e-06 6.563661e-14 1.260716e-13 1.659489e-13 7.817914e-12
62 2.046485e+04 -2.984034e+00 1.489794e-06 4.275136e-14 1.315134e-13 9.863714e-14 5.815667e-12
63 2.077969e+04 -2.888253e+00 8.864073e-07 2.107301e-14 1.053168e-13 4.595312e-14 3.655108e-12
64 2.109453e+04 -3.077504e+00 5.232797e-07 8.675422e-15 6.905988e-14 1.760052e-14 2.341958e-12
65 2.140938e+04 -3.169650e+00 3.201423e-07 3.365656e-15 3.595022e-14 6.162002e-15 1.394190e-12
66 2.172422e+04 -3.103242e+00 1.856889e-07 1.293778e-15 1.860925e-14 2.033915e-15 8.039162e-13
67 2.203907e+04 -3.195011e+00 1.027709e-07 3.343978e-16 5.949844e-15 5.858914e-16 4.132950e-13
68 2.235391e+04 -3.304330e+00 5.443506e-08 7.937542e-17 1.640208e-15 1.396395e-16 1.943107e-13
69 2.266875e+04 -3.441502e+00 2.939781e-08 1.475479e-17 3.430180e-16 4.586563e-17 9.063403e-14
70 2.298360e+04 -3.453566e+00 1.464506e-08 2.619737e-18 6.785903e-17 1.021336e-17 3.857130e-14
11 changes: 9 additions & 2 deletions tardis/io/tests/test_ascii_readers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,8 @@ def test_simple_ascii_abundance_reader():
(0.0 * u.km/u.s, np.inf * u.km/u.s, np.nan, np.nan, None, None),
(500 * u.km/u.s, 6000 * u.km/u.s, np.nan, 6000 * u.km/u.s, None, 16),
(1300 * u.km/u.s, 6000 * u.km/u.s, 1300 * u.km/u.s, 6000 * u.km/u.s, 0, 16),
(1600 * u.km/u.s, 6000 * u.km/u.s, 1600 * u.km/u.s, 6000 * u.km/u.s, 1, 16)
(1600 * u.km/u.s, 6000 * u.km/u.s, 1600 * u.km/u.s, 6000 * u.km/u.s, 1, 16),
(1889.063 * u.km/u.s, np.inf * u.km/u.s, 1889.063 * u.km/u.s, np.nan, 2, None)
])
def test_ascii_reader_density_boundaries(v_inner_boundary, v_outer_boundary, actual_v_inner, actual_v_outer,
inner_index, outer_index):
Expand All @@ -55,6 +56,12 @@ def test_ascii_reader_density_boundaries(v_inner_boundary, v_outer_boundary, act
actual_v_inner.to(v_inner[0].unit).value)

if not np.isnan(actual_v_outer):
npt.assert_allclose(v_outer[-1],
npt.assert_allclose(v_outer[-1].value,
actual_v_outer.to(v_outer[-1].unit).value)

def test_ascii_reader_invalid_volumes():

with pytest.raises(io.model_reader.ConfigurationError):
v_inner, v_outer, mean_densities, inner_boundary_index, outer_boundary_index = \
io.read_density_file(data_path('invalid_artis_model.dat'), 'artis', 19 *
u.day, 0.0 * u.km/u.s, np.inf * u.km/u.s)

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