(no subject)

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

(no subject)

Xiaosong Zhu

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
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users
Reply | Threaded
Open this post in threaded view
|

Re: (no subject)

Benjamin Root
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 <[hidden email]> 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
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users

_______________________________________________
Matplotlib-users mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users
Reply | Threaded
Open this post in threaded view
|

Re: (no subject)

Xiaosong Zhu

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

 

发件人: [hidden email]
发送时间: 20181127 22:20
收件人: [hidden email]
抄送: [hidden email]
主题: 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 <[hidden email]> 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
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users

 


_______________________________________________
Matplotlib-users mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users
Reply | Threaded
Open this post in threaded view
|

Re: (no subject)

Benjamin Root
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.

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 <[hidden email]> 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

 

发件人: [hidden email]
发送时间: 20181127 22:20
收件人: [hidden email]
抄送: [hidden email]
主题: 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 <[hidden email]> 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
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users

 


_______________________________________________
Matplotlib-users mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users
Reply | Threaded
Open this post in threaded view
|

Re: (no subject)

Xiaosong Zhu

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

 

 

发件人: [hidden email]
发送时间: 20181127 22:50
收件人: [hidden email]
抄送: [hidden email]
主题: 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.

 

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 <[hidden email]> 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

 

发件人: [hidden email]
发送时间: 20181127 22:20
收件人: [hidden email]
抄送: [hidden email]
主题: 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 <[hidden email]> 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
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users

 

 


_______________________________________________
Matplotlib-users mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/matplotlib-users