Tutorial mesh generation did not complete
ninjamongeese opened this issue · comments
While generating mesh, i get the following error:
C:\ProgramData\anaconda3\lib\site-packages\scipy\optimize\_minpack_py.py:178: RuntimeWarning: The iteration is not making good progress, as measured by the
improvement from the last five Jacobian evaluations.
warnings.warn(msg, RuntimeWarning)
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[8], line 1
----> 1 Mesh(
2 sim=sim,
3 metal_res=1 / 80,
4 nonmetal_res=1 / 40,
5 smooth=(1.1, 1.5, 1.5),
6 min_lines=5,
7 expand_bounds=((0, 0), (0, 0), (10, 40)),
8 )
File C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:594, in Mesh.__init__(self, sim, metal_res, nonmetal_res, smooth, min_lines, expand_bounds, simulation_bounds)
591 # set later
592 self.bounded_types = None
--> 594 self.generate_mesh()
File C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:619, in Mesh.generate_mesh(self, show_pml)
617 self._gen_mesh_for_bounded_types(self.size_ordered_bounded_types)
618 self._trim_air_mesh()
--> 619 self._smooth_pml_mesh_lines()
621 self._set_mesh_from_lines()
622 if show_pml:
File C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:722, in Mesh._smooth_pml_mesh_lines(self)
717 spacing = limit_spacing * smooth_factor
718 elif (
719 spacing < limit_spacing
720 and limit_spacing / spacing >= smooth_factor
721 ):
--> 722 raise RuntimeError(
723 "PML mesh smoothing is increasing the simulation "
724 "box size. This should never happen. Either "
725 "structures in your PML are non-uniform in the "
726 "direction of the PML in which case you'll get an "
727 "error anyway, or this is a bug in pyems."
728 )
730 # only smooth lines if necessary
731 if np.isclose(spacing, limit_spacing, rtol=1e-3, atol=0):
RuntimeError: PML mesh smoothing is increasing the simulation box size. This should never happen. Either structures in your PML are non-uniform in the direction of the PML in which case you'll get an error anyway, or this is a bug in pyems.
3.10.9 | packaged by Anaconda, Inc. | (main, Mar 1 2023, 18:18:15) [MSC v.1916 64 bit (AMD64)]
U:>conda list
packages in environment at C:\Users\All Users\anaconda3:
Name Version Build Channel
alabaster 0.7.12 pyhd3eb1b0_0
anaconda-anon-usage 0.4.0 py310h8ddfbff_0
anaconda-client 1.11.2 py310haa95532_0
anaconda-navigator 2.4.3 py310haa95532_0
anaconda-project 0.11.1 py310haa95532_0
anyio 3.5.0 py310haa95532_0
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py310h2bbff1b_0
arrow 1.2.3 py310haa95532_1
astroid 2.14.2 py310haa95532_0
astropy 5.1 py310h9128911_0
asttokens 2.0.5 pyhd3eb1b0_0
atomicwrites 1.4.0 py_0
attrs 22.1.0 py310haa95532_0
automat 20.2.0 py_0
autopep8 1.6.0 pyhd3eb1b0_1
babel 2.11.0 py310haa95532_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.1 pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
bcrypt 3.2.0 py310h2bbff1b_1
beautifulsoup4 4.11.1 py310haa95532_0
binaryornot 0.4.4 pyhd3eb1b0_1
black 22.6.0 py310haa95532_0
blas 1.0 mkl
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bokeh 2.4.3 py310haa95532_0
boltons 23.0.0 py310haa95532_0
bottleneck 1.3.5 py310h9128911_0
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brotlipy 0.7.0 py310h2bbff1b_1002
bzip2 1.0.8 he774522_0
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chardet 4.0.0 py310haa95532_1003
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click 8.0.4 py310haa95532_0
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future 0.18.3 py310haa95532_0
gensim 4.3.0 py310h4ed8f06_0
giflib 5.2.1 h8cc25b3_3
glib 2.69.1 h5dc1a3c_2
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greenlet 2.0.1 py310hd77b12b_0
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h5py 3.7.0 py310hfc34f40_0
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imageio 2.26.0 py310haa95532_0
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importlib-metadata 4.11.3 py310haa95532_0
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intel-openmp 2021.4.0 haa95532_3556
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jpeg 9e h2bbff1b_1
jq 1.6 haa95532_1
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jsonschema 4.17.3 py310haa95532_0
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jupyter_client 7.3.4 py310haa95532_0
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libclang 12.0.0 default_h627e005_2
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mkl 2021.4.0 haa95532_640
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nest-asyncio 1.5.6 py310haa95532_0
networkx 2.8.4 py310haa95532_0
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nltk 3.7 pyhd3eb1b0_0
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numpy 1.23.5 py310h60c9a35_0
numpy-base 1.23.5 py310h04254f7_0
numpydoc 1.5.0 py310haa95532_0
openems 0.0.33 pypi_0 pypi
openjpeg 2.4.0 h4fc8c34_0
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openssl 1.1.1w h2bbff1b_0
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param 1.12.3 py310haa95532_0
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parso 0.8.3 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_1
pathlib 1.0.1 pyhd3eb1b0_1
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pcre 8.45 hd77b12b_0
pep8 1.7.1 py310haa95532_1
pexpect 4.8.0 pyhd3eb1b0_3
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py 1.11.0 pyhd3eb1b0_0
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pyparsing 3.0.9 py310haa95532_0
pyqt 5.15.7 py310hd77b12b_0
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pysocks 1.7.1 py310haa95532_0
pytables 3.7.0 py310h388bc9b_1
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python 3.10.9 h966fe2a_1
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scikit-image 0.19.3 py310hd77b12b_1
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sqlite 3.40.1 h2bbff1b_0
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sympy 1.11.1 py310haa95532_0
tabulate 0.8.10 py310haa95532_0
tbb 2021.7.0 h59b6b97_0
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tblib 1.7.0 pyhd3eb1b0_0
tenacity 8.0.1 py310haa95532_1
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three-merge 0.1.1 pyhd3eb1b0_0
tifffile 2021.7.2 pyhd3eb1b0_2
tinycss2 1.2.1 py310haa95532_0
tk 8.6.12 h2bbff1b_0
tldextract 3.2.0 pyhd3eb1b0_0
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toml 0.10.2 pyhd3eb1b0_0
tomli 2.0.1 py310haa95532_0
tomlkit 0.11.1 py310haa95532_0
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tornado 6.1 py310h2bbff1b_0
tqdm 4.64.1 py310haa95532_0
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transformers 4.24.0 py310haa95532_0
twisted 22.2.0 py310h2bbff1b_1
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typing-extensions 4.4.0 py310haa95532_0
typing_extensions 4.4.0 py310haa95532_0
tzdata 2022g h04d1e81_0
ujson 5.4.0 py310hd77b12b_0
unidecode 1.2.0 pyhd3eb1b0_0
urllib3 1.26.14 py310haa95532_0
vc 14.2 h21ff451_1
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w3lib 1.21.0 pyhd3eb1b0_0
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wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py310haa95532_1
websocket-client 0.58.0 py310haa95532_4
werkzeug 2.2.2 py310haa95532_0
whatthepatch 1.0.2 py310haa95532_0
wheel 0.38.4 py310haa95532_0
widgetsnbextension 3.5.2 py310haa95532_0
win_inet_pton 1.1.0 py310haa95532_0
wincertstore 0.2 py310haa95532_2
winpty 0.4.3 4
wrapt 1.14.1 py310h2bbff1b_0
xarray 2022.11.0 py310haa95532_0
xlwings 0.29.1 py310haa95532_0
xz 5.2.10 h8cc25b3_1
yaml 0.2.5 he774522_0
yapf 0.31.0 pyhd3eb1b0_0
zeromq 4.3.4 hd77b12b_0
zfp 0.5.5 hd77b12b_6
zict 2.1.0 py310haa95532_0
zipp 3.11.0 py310haa95532_0
zlib 1.2.13 h8cc25b3_0
zope 1.0 py310haa95532_1
zope.interface 5.4.0 py310h2bbff1b_0
zstandard 0.19.0 py310h2bbff1b_0
zstd 1.5.2 h19a0ad4_0
Please specify the example you're running.
The front page example. I guess looking at the code page its actually labelled "Tutorial". Hope that helps!
This error seems to be related to the argument
Mesh(expand_bounds=((0, 0), (0, 0), (10, 40)))
I took out that argument entirely as a test, as I'm unsure what maximum Z height is of the simulation for this configuration. When I take out just that argument to let it use the default parameters, i was able to get that step to run. It generated a mesh but with some warnings. Not sure if its related or even an issue. warnings below:
C:\ProgramData\anaconda3\lib\site-packages\scipy\optimize\_minpack_py.py:178: RuntimeWarning: The iteration is not making good progress, as measured by the
improvement from the last five Jacobian evaluations.
warnings.warn(msg, RuntimeWarning)
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos -5.8817 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.12. For convenience the last three lines are: -6.2229, -6.0423 and -5.8817.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos -5.5787 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.13. For convenience the last three lines are: -5.8817, -5.7212 and -5.5787.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos -4.3335 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.15. For convenience the last three lines are: -4.4190, -4.3732 and -4.3335.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos -3.9962 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.28. For convenience the last three lines are: -4.0150, -4.0045 and -3.9962.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos -3.9614 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.24. For convenience the last three lines are: -3.9798, -3.9716 and -3.9614.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos 3.9798 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.24. For convenience the last three lines are: 3.9614, 3.9716 and 3.9798.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos 4.0150 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.28. For convenience the last three lines are: 3.9962, 4.0045 and 4.0150.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos 4.4190 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.15. For convenience the last three lines are: 4.3335, 4.3732 and 4.4190.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos 5.8817 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.13. For convenience the last three lines are: 5.5787, 5.7212 and 5.8817.
C:\ProgramData\anaconda3\lib\site-packages\pyems-0.1.0-py3.10.egg\pyems\mesh.py:664: UserWarning: Mesh line at pos 6.2229 for dimension 0 violates smoothness. Smoothness was set to 1.10 but this line creates a spacing with factor 1.12. For convenience the last three lines are: 5.8817, 6.0423 and 6.2229.
Got it. Thanks for the bug report I'll take a look in a couple days (can't this weekend).
Those warnings aren't necessarily a problem; they merely indicate that the mesher can’t meet the constraints you've set (or I suppose the ones I set, since it's the tutorial). When you're writing your own simulations, you'll find this crop up and often it means you just were a bit too strict with the mesh requirements and the mesh is still good. If you deem the mesh result inadequate, though, you'll have to adjust the design in some respect so the requirements can be met.