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
Date: Wed, Jan 22, 2020 at 12:22 PM
Subject: Re: Some questions on the viewer
To: Guyer, Jonathan E. Dr. (Fed) ,
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:
[image: 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 <
[email protected]> 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 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 <
> [email protected]> 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 prac
