(no subject)

Hi Everyone!

May I ask a question. Is it possible to plot the 3D iso-surface figures? Like the figures plotted by isosurface in MATLAB?

https://www.mathworks.com/help/matlab/ref/isosurface.html

Or like the 1st figure in

https://en.wikipedia.org/wiki/Atomic_orbital.

I need this because I would like to plot the configure of target molecular orbitals using the data calculated from first-principle calculation. I have looked through the examples of the website. There are only examples similar to this but not the same?

Thanks very much!

Sincerely,
Xiaosong
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plot_surface() in mplot3d can ultimately do what you want, but you need to
provide it the isosurface. I think scikit-image can provide that
information with its marching cubes function.

Does that help?

Ben Root

···

On Tue, Nov 27, 2018 at 4:05 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:

Hi Everyone!

May I ask a question. Is it possible to plot the 3D iso-surface figures?
Like the figures plotted by isosurface in MATLAB?

https://www.mathworks.com/help/matlab/ref/isosurface.html

Or like the 1st figure in

https://en.wikipedia.org/wiki/Atomic_orbital.

I need this because I would like to plot the configure of target molecular
orbitals using the data calculated from first-principle calculation. I have
looked through the examples of the website. There are only examples similar
to this but not the same?

Thanks very much!

Sincerely,

Xiaosong
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

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Dear Ben,

Thank you very much! I guess so and I will check that! I previously saw some examples but thought colour could only be the same at the same height. But this may not be true. The cubes may be also helpful!

Thank you very much for your help!

Sincerely,
Xiaosong

???: Benjamin Root
???: 2018?11?27? 22:20
???: zxs.201 at gmail.com
??: Matplotlib-users
??: Re: [Matplotlib-users] (no subject)

plot_surface() in mplot3d can ultimately do what you want, but you need to provide it the isosurface. I think scikit-image can provide that information with its marching cubes function.

Does that help?

Ben Root

···

On Tue, Nov 27, 2018 at 4:05 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:
Hi Everyone!
?
May I ask a question. Is it possible to plot the 3D iso-surface figures? Like the figures plotted by isosurface in MATLAB?
?
https://www.mathworks.com/help/matlab/ref/isosurface.html
?
Or like the 1st figure in
?
https://en.wikipedia.org/wiki/Atomic_orbital.
?
I need this because I would like to plot the configure of target molecular orbitals using the data calculated from first-principle calculation. I have looked through the examples of the website. There are only examples similar to this but not the same?
?
Thanks very much!
?
Sincerely,
Xiaosong
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

-------------- next part --------------
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The default settings for plot_surface() yields an surface with the same
color. There are multiple ways to color the surface, either by supplying
color information yourself via "facecolors", or turning on the "shade",
and/or providing a "lightsource" object for custom shading. Unfortunately,
the docs are pretty sparse in this area, but hopefully this will help.

https://matplotlib.org/api/_as_gen/mpl_toolkits.mplot3d.axes3d.Axes3D.html#mpl_toolkits.mplot3d.axes3d.Axes3D.plot_surface
There are some examples of using some of these keyword arguments here:
https://matplotlib.org/examples/mplot3d/index.html

Ben Root

···

On Tue, Nov 27, 2018 at 4:34 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:

Dear Ben,

Thank you very much! I guess so and I will check that! I previously saw
some examples but thought colour could only be the same at the same height.
But this may not be true. The cubes may be also helpful!

Thank you very much for your help!

Sincerely,

Xiaosong

*???: *Benjamin Root <ben.v.root at gmail.com>
*???: *2018?11?27? 22:20
*???: *zxs.201 at gmail.com
*??: *Matplotlib-users <matplotlib-users at python.org>
*??: *Re: [Matplotlib-users] (no subject)

plot_surface() in mplot3d can ultimately do what you want, but you need to
provide it the isosurface. I think scikit-image can provide that
information with its marching cubes function.

Does that help?

Ben Root

On Tue, Nov 27, 2018 at 4:05 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:

Hi Everyone!

May I ask a question. Is it possible to plot the 3D iso-surface figures?
Like the figures plotted by isosurface in MATLAB?

https://www.mathworks.com/help/matlab/ref/isosurface.html

Or like the 1st figure in

https://en.wikipedia.org/wiki/Atomic_orbital.

I need this because I would like to plot the configure of target molecular
orbitals using the data calculated from first-principle calculation. I have
looked through the examples of the website. There are only examples similar
to this but not the same?

Thanks very much!

Sincerely,

Xiaosong

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

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Dear Ben,

Thank you very much! Now that I know it is possible, I will carefully read the manual and solve the problem!

Sincerely,
Xiaosong

???: Benjamin Root
???: 2018?11?27? 22:50
???: zxs.201 at gmail.com
??: Matplotlib-users
??: Re: [Matplotlib-users] (no subject)

The default settings for plot_surface() yields an surface with the same color. There are multiple ways to color the surface, either by supplying color information yourself via "facecolors", or turning on the "shade", and/or providing a "lightsource" object for custom shading. Unfortunately, the docs are pretty sparse in this area, but hopefully this will help.

https://matplotlib.org/api/_as_gen/mpl_toolkits.mplot3d.axes3d.Axes3D.html#mpl_toolkits.mplot3d.axes3d.Axes3D.plot_surface
There are some examples of using some of these keyword arguments here: https://matplotlib.org/examples/mplot3d/index.html

Ben Root

···

On Tue, Nov 27, 2018 at 4:34 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:
Dear Ben,
?
Thank you very much! I guess so and I will check that! I previously saw some examples but thought colour could only be the same at the same height. But this may not be true. The cubes may be also helpful!
?
Thank you very much for your help!
?
Sincerely,
Xiaosong
?
???: Benjamin Root
???: 2018?11?27? 22:20
???: zxs.201 at gmail.com
??: Matplotlib-users
??: Re: [Matplotlib-users] (no subject)
?
plot_surface() in mplot3d can ultimately do what you want, but you need to provide it the isosurface. I think scikit-image can provide that information with its marching cubes function.
?
Does that help?
?
Ben Root
?
?
On Tue, Nov 27, 2018 at 4:05 PM Xiaosong Zhu <zxs.201 at gmail.com> wrote:
Hi Everyone!
?
May I ask a question. Is it possible to plot the 3D iso-surface figures? Like the figures plotted by isosurface in MATLAB?
?
https://www.mathworks.com/help/matlab/ref/isosurface.html
?
Or like the 1st figure in
?
https://en.wikipedia.org/wiki/Atomic_orbital.
?
I need this because I would like to plot the configure of target molecular orbitals using the data calculated from first-principle calculation. I have looked through the examples of the website. There are only examples similar to this but not the same?
?
Thanks very much!
?
Sincerely,
Xiaosong
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users
?

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