Hi Jon, It looks like pyvista *does* support VTK_CONVEX_POINT_SET. Please take a look at the discussion I started on https://github.com/pyvista/pyvista-support/issues/108
They are claiming that fipy's mesh might be ill-formed which I am a bit skeptical about. For instance I think Grid2D works fine, but for some reason I still get a blank plot with pyvista. A contribution from the fipy team on the above discussion would be most useful. If there is a resolution I'd be happy to take a look at submitting a pull request for a pyvista-enabled Viewer class, though I may need some guidance in order not to break things. Regards, Amine On Wed, Jan 22, 2020 at 6:19 PM Guyer, Jonathan E. Dr. (Fed) via fipy < fipy@nist.gov> wrote: > FiPy can have completely general polyhedral cells, whereas VTK is more > restrictive. In principle, VTK_CONVEX_POINT_SET allows the same generality, > but as you've seen, this cell type is not implemented by many tools using > VTK. > > General 2D meshes know to export VTK_POLYGONs, which are widely understood. > > 2D grids bypass this specialization for historical reasons and so just get > the default VTK_CONVEX_POINT_SET. We've never had any call to render 2D > grids with VTK tools, so we've not noticed this before. Grid meshes should > be exported as VTK_PIXEL or VTK_VOXEL. Fixing in this in FiPy is likely to > happen sooner than getting any of those other packages to support > VTK_CONVEX_POINT_SET. I have a (stalled) development that does a better job > with mesh io, but higher priority tasks have gotten in the way. > > > On Jan 22, 2020, at 10:11 AM, A A <amine.aboufir...@gmail.com> wrote: > > > > > > This is somewhat related to my last comment about visualizing meshes. > I'm noticing that both CylindricalGrid2D and Grid2D default to a cell type > of 41 which according to VTK is a VTK_CONVEX_POINT_SET (see > https://vtk.org/doc/nightly/html/vtkCellType_8h_source.html). > Interestingly, the mesh generated in fipy's circle diffusion example using > gmesh capability results in a mesh of cell type 7 which is a VTK_POLYGON. > I'm suspecting that the third party libraries I'm using to plot these > meshes might be limited to cell types with numbers ranging from 0 to 35 > thus not including fipy's choice of cell type 41. > > > > Is the choice of the cell type intentional or important here? If so it > might be worth convincing those libraries to add cell type 41 plotting and > i/o capabilities. > > ---------- Forwarded message --------- > > From: A A <amine.aboufir...@gmail.com> > > Date: Wed, Jan 22, 2020 at 12:22 PM > > Subject: Re: Some questions on the viewer > > To: Guyer, Jonathan E. Dr. (Fed) <jonathan.gu...@nist.gov>, < > fipy@nist.gov> > > > > > > Hi Jonathan, > > > > The lines do remain dashed on successive calls. I guess the viewer keeps > pointing to the right objects even if their properties are retroactively > modified. > > > > Here's what I mean about the diffusion term: > > > > <Untitled.png> > > > > On another note, I've posted some stuff on github which may be of > interest regarding the circle diffusion example. I had a hard time > visualizing the mesh so I went with some third-party packages (pyvista, > pygmsh) and the result looks quite nice. > https://github.com/usnistgov/fipy/issues/693 > > > > I'm now experimenting with cylindrical coordinates as I would like to > try to solve the heat equation in radial terms. I tried repeating the above > procedure to visualize CylindricalGrid1D and CylindricalGrid2D objects but > without much luck. Here's what I'm doing: > > > > from fipy import Variable, FaceVariable, CellVariable, Grid1D, > CylindricalGrid1D, CylindricalGrid2D, ExplicitDiffusionTerm, TransientTerm, > DiffusionTerm, Viewer > > from fipy.tools import numerix > > import numpy as np > > import pyvista > > > > mesh = CylindricalGrid2D(dr=0.1, dz=0.25, nr=3, nz=0.1) > > ugrid= pyvista.UnstructuredGrid(mesh.VTKCellDataSet._vtk_obj) > > plotter = pyvista.Plotter() > > plotter.set_background('white') > > plotter.add_mesh(ugrid, style='wireframe', color='black') > > plotter.add_bounding_box(color='red') > > plotter.show_grid(color="red") > > plotter.view_xy() > > plotter.show() > > > > I only get the red bounding box/grid but no cylindrical mesh. Is there > something I'm missing regarding the nature of CylindricalGrid objects? It > seems that fipy is working with/using VTK under the hood so it would be > nice to be able to recover it and take a look at what I'm working with... > > > > Regards, > > > > Amine > > > > On Tue, Jan 21, 2020 at 3:55 PM Guyer, Jonathan E. Dr. (Fed) via fipy < > fipy@nist.gov> wrote: > > I'm curious. Do the lines remain dashed on successive calls to plot()? > > > > As to the third question, where are you seeing exponent n and subscript > i? I'm not suggesting we don't use them, just that I don't know where. > > > > Is the discussion at > > > https://www.ctcms.nist.gov/fipy/documentation/numerical/discret.html#higher-order-diffusion > > helpful? > > > > > On Jan 21, 2020, at 1:25 AM, A A <amine.aboufir...@gmail.com> wrote: > > > > > > Hi Martin, > > > > > > Thanks for your response. That's strange that such a "dummy" command > would be necessary. > > > > > > I was able to answer the second question myself. It is possible to > retroactively change line and axis properties. For the mesh1D example I did > the following: > > > > > > viewer = Viewer(vars=(phi, phi_analytical), datamin=-6.0, datamax=6.0) > > > ax = viewer.axes > > > ax.lines[-1].set_dashes((3.5,3.5,3.5,3.5)) > > > ax.grid() > > > viewer.plot() > > > > > > Which seemed to work quite well. > > > > > > With regards to the third question, I think the terms in the general > conservation equation are explained reasonably well in the fipy docs, > except for the diffusion term. It is unclear what the exponent n and > subscript i represent and how they are related to one another. Is the > exponent an arithmetic exponent? Is i part of a sum? I had trouble > expanding the diffusion term to n>=4. > > > > > > Regards, > > > > > > Amine > > > > > > On Mon, Jan 20, 2020 at 5:23 PM Martinus WERTS < > martinus.we...@ens-rennes.fr> wrote: > > > Dear Amine, > > > > > > Concerning your second question, I think that this a normal (but in > this case, annoying) feature of the Jupyter notebook. > > > > > > You might trying adding an extra (dummy) command to the cell, after > the line in which the Viewer() is instantiated. For example: > ``print('Ready')``. > > > > > > Best, > > > Martin > > > > > > On 20/01/2020 17:01, A A wrote: > > >> Dear All, > > >> > > >> I'm just getting back into using fipy after a few months hiatus. I'm > getting more familiar with how it works, but I have a couple of questions > about the viewer: > > >> • Is it possible to control linestyle (specifically dashes) of > the cellVariable objects tied to each specific viewer? I'd like to avoid > the possibility of superimposing very similar plots and thinking they are > the same > > >> • I am primarily using jupyter notebook to practice some basic > concepts. What I've found is that simply instantiating the viewer in > interactive mode will generate a plot. This renders a viewer.plot() call > redundant. When I run the whole notebook in non-interactive mode I get the > expected behavior, namely one plot with a .plot() call. Am I missing > something here? Why does viewer instantiation generate a plot in jupyter > notebook? > > >> Thanks for your help and look forward to your reply. > > >> > > >> Regards, > > >> > > >> Amine Aboufirass > > >> > > >> > > >> _______________________________________________ > > >> fipy mailing list > > >> > > >> fipy@nist.gov > > >> http://www.ctcms.nist.gov/fipy > > >> > > >> [ NIST internal ONLY: > > >> https://email.nist.gov/mailman/listinfo/fipy > > >> ] > > >> > > > > > > > > > _______________________________________________ > > > fipy mailing list > > > fipy@nist.gov > > > http://www.ctcms.nist.gov/fipy > > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > _______________________________________________ > > > fipy mailing list > > > fipy@nist.gov > > > http://www.ctcms.nist.gov/fipy > > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > > > > _______________________________________________ > > fipy mailing list > > fipy@nist.gov > > http://www.ctcms.nist.gov/fipy > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > _______________________________________________ > > fipy mailing list > > fipy@nist.gov > > http://www.ctcms.nist.gov/fipy > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >
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