VMD-L Mailing List

From: CHEN, Chi (cchenae_at_ust.hk)
Date: Tue Oct 01 2013 - 03:08:42 CDT

Dear axel,

I apologize for not responding to the list.
Thanks very much for your response. It indeed solved the problem.

Cheers

CC

-----邮件原件-----
发件人: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
发送时间: 2013年10月1日 15:58
收件人: CHEN, Chi; Vmd l
主题: Re: 答复: vmd-l: How to show section contour of volumetric data

please always respond to the mailing list, to that people get to see the
replies and can look up the resolution in the future, if they run into the
same issue. thanks.

On Tue, Oct 1, 2013 at 9:47 AM, CHEN, Chi <cchenae_at_ust.hk> wrote:
> Dear Axel,
> Thanks for your quick response.
> I used VESTA to produce the figure I described and succeeded.
> I was just wondering if there is a way to do that in VMD, because I
> saw in one paper they used VMD.
> http://pubs.rsc.org/en/content/articlehtml/2010/cp/c001809k

> I thought it was high level vmd technique. That's why I ask.

this is a much simpler issue and that is indeed possible with VMD plus some
postprocessing. i would create that kind of picture through
"greenscreening", i.e. you create two images from the same setup. the first
you create with the regular isosurface. in the second you have solid box
walls and colormap the volumetric data set on it. in the color scale, you
use one specific color (e.g. purple, cyan, magenta or white or gray) that is
not otherwise present for the part of the box surface, that you want to cut
away. you render both images and load them into gimp or photoshop and then
do a "select-by-color" on the second image, cut away the unwanted part and
overlay this image to the first. voila!

axel.

> Thank you very much again.
>
> Chi
>
>
> -----邮件原件-----
> 发件人: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> 发送时间: 2013年10月1日 15:21
> 收件人: CHEN, Chi
> 抄送: vmd-l_at_ks.uiuc.edu
> 主题: Re: vmd-l: How to show section contour of volumetric data
>
> On Tue, Oct 1, 2013 at 3:57 AM, CHEN, Chi <cchenae_at_ust.hk> wrote:
>> Dear All,
>> Thanks for taking your time reading this.
>> I have a volumetric density data generated by volmap plugin. I know
>> how to show the isosurface, but only the isosurface is not very
>> pleasing,
> since the cross section of the volumetric data is not shown, which
> makes the isosurface a little weird. By cross section, i mean for
> example if we use a clip plane, we can cut the isosurface, creating a
> hollow cross section. There is a volumeslice method which does almost
> what I want, but it shows the whole slice plane instead of the part
> it intersects with the isosurface.
>
> there actually is no real question here, but it seems what you want is
> to have an option to "close" an isosurface, when you place a cutting
> plane through it (the colorization is independent of that).
>
> that option does not exist. to have that, you need to look into using
> a visualization tool that is more grid data oriented (and less
> molecular), e.g. paraview, visit, opendx, etc.
>
> axel.
>
>
>>
>> I hope this is clear.
>>
>> Thanks
>>
>> Chi
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0 International
Centre for Theoretical Physics, Trieste. Italy.