FVM_Cylinder_GMsh.ipynb returns KeyError: ('cells', False)

[StuvX]

When I try to run FVM_Cylinder_GMsh.ipynb I get the following error:

---

KeyError Traceback (most recent call last)
File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/IPython/core/formatters.py:347, in BaseFormatter.call(self, obj)
345 method = get_real_method(obj, self.print_method)
346 if method is not None:
--> 347 return method()
348 return None
349 else:

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/matplotlib/animation.py:1362, in Animation.repr_html(self)
1360 fmt = mpl.rcParams['animation.html']
1361 if fmt == 'html5':
-> 1362 return self.to_html5_video()
1363 elif fmt == 'jshtml':
1364 return self.to_jshtml()

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/matplotlib/animation.py:1289, in Animation.to_html5_video(self, embed_limit)
1285 Writer = writers[mpl.rcParams['animation.writer']]
1286 writer = Writer(codec='h264',
1287 bitrate=mpl.rcParams['animation.bitrate'],
1288 fps=1000. / self._interval)
-> 1289 self.save(str(path), writer=writer)
1290 # Now open and base64 encode.
1291 vid64 = base64.encodebytes(path.read_bytes())

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/matplotlib/animation.py:1092, in Animation.save(self, filename, writer, fps, dpi, codec, bitrate, extra_args, metadata, extra_anim, savefig_kwargs, progress_callback)
1089 with writer.saving(self._fig, filename, dpi),
1090 cbook._setattr_cm(self._fig.canvas, _is_saving=True, manager=None):
1091 for anim in all_anim:
-> 1092 anim._init_draw() # Clear the initial frame
1093 frame_number = 0
1094 # TODO: Currently only FuncAnimation has a save_count
1095 # attribute. Can we generalize this to all Animations?

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/matplotlib/animation.py:1749, in FuncAnimation._init_draw(self)
1741 warnings.warn(
1742 "Can not start iterating the frames for the initial draw. "
1743 "This can be caused by passing in a 0 length sequence "
(...)
1746 "it may be exhausted due to a previous display or save."
1747 )
1748 return
-> 1749 self._draw_frame(frame_data)
1750 else:
1751 self._drawn_artists = self._init_func()

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/matplotlib/animation.py:1768, in FuncAnimation._draw_frame(self, framedata)
1764 self._save_seq = self._save_seq[-self._save_count:]
1766 # Call the func with framedata and args. If blitting is desired,
1767 # func needs to return a sequence of any artists that were modified.
-> 1768 self._drawn_artists = self._func(framedata, *self._args)
1770 if self._blit:
1772 err = RuntimeError('The animation function must return a sequence '
1773 'of Artist objects.')

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/phi/vis/_matplotlib/_matplotlib_plots.py:157, in MatplotlibPlots.animate..clear_and_plot(frame)
154 axis.set_subplotspec(specs[axis])
155 # subplot.set_title(titles[subplot])
156 # plt.tight_layout()
--> 157 plot_frame_function(frame)

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/phi/vis/_vis.py:399, in plot..plot_frame(frame)
397 for i, f in enumerate(fields):
398 idx = indices[pos][i]
--> 399 f = f[{animate.name: frame}]
400 plots.plot(f, figure, axes[pos], subplots[pos], min_val, max_val, show_color_bar, color[idx], alpha[idx], err[idx])
401 plots.finalize(figure)

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/phi/field/_field.py:641, in Field.getitem(self, item)
639 if not item:
640 return self
--> 641 boundary = domain_slice(self._boundary, item, self.resolution)
642 item_without_vec = {dim: selection for dim, selection in item.items() if dim != 'vector'}
643 geometry = self._geometry[item_without_vec]

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/phiml/math/extrapolation.py:1791, in domain_slice(ext, item, domain_dims)
1789 domain_dims = parse_dim_order(domain_dims)
1790 for dim in domain_dims:
-> 1791 lo = ext._getitem_with_domain(item, dim, False, domain_dims)
1792 up = ext._getitem_with_domain(item, dim, True, domain_dims)
1793 if lo == up:

File ~/miniconda3/envs/grow2/lib/python3.10/site-packages/phiml/math/extrapolation.py:1343, in _MixedExtrapolation._getitem_with_domain(self, item, dim, upper_edge, all_dims)
1341 if b in [dim, dim+('+' if upper_edge else '-')]:
1342 return ext._getitem_with_domain(item, b[:-1], b.endswith('+'), all_dims)
-> 1343 raise KeyError((dim, upper_edge))

KeyError: ('cells', False)

[holl-]

Hey, thanks for the bug report! I'll look into it soon. In the meantime, could you check whether this still occurs with the latest version 3.1.0?
pip install --upgrade phiflow

[StuvX]

Now I receive the following error:

/usr/local/lib/python3.10/dist-packages/phiml/backend/torch/_torch_backend.py:800: UserWarning: Sparse CSR tensor support is in beta state. If you miss a functionality in the sparse tensor support, please submit a feature request to https://github.com/pytorch/pytorch/issues. (Triggered internally at ../aten/src/ATen/SparseCsrTensorImpl.cpp:53.)
return torch.sparse_csr_tensor(row_pointers, column_indices, values, shape, device=values.device)

---

AssertionError Traceback (most recent call last)

in <cell line: 4>()
2 boundary = {'x-': wind, 'x+': ZERO_GRADIENT, 'y': 0, 'cyl': 0}#, 'cells': True}
3 velocity = Field(mesh, tensor(vec(x=0, y=0)), boundary)
----> 4 v_trj = math.iterate(implicit_time_step, batch(time=100), velocity, dt=0.001, range=trange)

4 frames

/usr/local/lib/python3.10/dist-packages/phi/field/_field_math.py in stack(fields, dim, dim_bounds)
950 return PointCloud(geometry, values, boundary)
951 elif fields[0].is_mesh:
--> 952 assert all([f.geometry == fields[0].geometry for f in fields]), f"stacking fields with different geometries is not supported. Got {[f.geometry for f in fields]}"
953 values = math.stack([f.values for f in fields], dim)
954 return Field(fields[0].geometry, values, boundary)

AssertionError: stacking fields with different geometries is not supported. Got [Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566, vectorᶜ=x,y), Mesh(cellsⁱ=10566,

[holl-]

It runs on my machine with the latest version. Could you try

pip uninstall phiflow phiml
pip install git+https://github.com/tum-pbs/PhiFlow@develop